The problems you describe don't exist in a guild of professional adult players.
The Armor Class (aka "Who Can Roll") Problem:
How does the loot system account for cloth caster items and leather melee items as upgrades for mail and plate classes?
The issue doesn't really exist. Armor class has no intrinsic value in vanilla wow. Except for tanks. Please come up with examples.
The Armor Slot (aka Hoarding) Problem:
How does the loot system deal with the fact that bracers and belts are worth far less than other slots?
(One of the biggest problems with the Suicide Kings system)
If loot is handed out in advance, it's easy to set up a rough order in which items are awarded. The best warrior gets the first Onslaught Girdle for example, but then doesn't get the 2nd best item first. Maybe 4th or 5th, depending on how much of a difference there is in raid performance, guild dedication, activity and ability to show on time with all mandatory consumables.
The Scarcity Problem:
How does the loot system encourage attendance with fewer items dropping?
(Much more of a problem for casual guilds where people may not attend if they know it's gonna be a month before they're eligible to win anything.
The scarcity of loot relative to retail also causes differences in loot distribution for people that know they're going to be out, for example people with newborns on the way or armed forces deployments.)
Membership status hinges on guild attendance. If a player fails to show, he or she can be demoted to social status until attendance can once again reach an acceptable level. It's the officers and guild masters task to have this talk, which may or may not be difficult if the person has been in the guild a long time. Preferably, you should initiate the talk yourself if you know you cannot show. Then show as a social to fill a spot if there is one every now and then.
The Progression / Farm Problem:
How does the loot system reward progression nights over farm nights?
(More a problem in vanilla where players can't just go get the Heroic / Normal / LFR version of that must-have trinket.)
All the raids remain mandatory progression paths for an exceedingly long time. Guilds progressing through Naxxramas may still want to run Molten core so their hunters can finally grab a Band of Accuria. At that point in progression, some people may have alts to gear up as well. With 2 raid nights, not showing for farm night means not showing for half the mandatory raids. 50% is not an acceptable attendance rate.
The Incentivization Problem:
Does the loot system reward bringing consumables to raid?
Loot distribution hinges on it. Obviously showing with fewer than ideal consumables due to unforeseen circumstances is better than not showing. But experienced players will gradually accumulate more consumables than they spend every week. I.e farm 125% of what you use, so that you are ahead if getting consumables is difficult a week. Continuously showing without the mandatory consumables will result in lower loot priority, and if a better player can be found, demotion to social.
The PUG Problem:
If it's not a full guild run, what incentives do PUGs have to come? If an item drops and Guildy A has it, Guildy B needs it, and PUG C needs it, does Guildy A get to roll and give it to guildy B if he wins?
Such discussions must be had in advance with the pugs. Presumably, a full guild run + some pugs, you know who these people are and can sort out some deal where the most sought after items goes to the guild. Such as Band of Accuria, Drake Fang Talisman etc. If you form a raid with pugs you don't know, the reputation of the guild is more important than some purple pixels. Loot rules must be made clear to everyone, and don't even attempt to deviate from the agreed upon rules.
The Main Tank Problem:
How does the loot system deal with the fact that in vanilla, there was both a strong incentive to give the main tank the best gear available but also an incentive to give warrior DPS the gear as well. At what point does a big upgrade to an off-tank offset a small upgrade to a main tank?
This is a non-issue. Each boss has a roughly equal chance to drop any of the items on the loot table, with few exceptions. With 1 main tank + 2 off-tanks, gearing up the tanks is completed far sooner than any other class. Unlike the 5-7 mages, 3-5 warlocks, 6-8 rogues, 6-8 fury warriors and 3-5 hunters.
The Tryhard / Slacker Problem:
How does the loot system deal with the fact that, especially in early tiers, there are powerful BoE items available? For example, Mace of +3 smiting drops. Player A farmed gold for months to buy the BoE Mace of +2 smiting. Player B didn't farm at all and has Questing Mace of +1 smiting. Who gets the item?
case by case. It's not an easy question to answer, but preferably both of the players in question would do their utmost to improve their character but also the guilds. If player 1 farms, and player 2 runs dungeon with guild to help them gear up. There is no real difference in time spent improving the overall performance of the guild. I know people helping guild members do over 100 BRD runs to get the Ironfoe mace, obviously sacrificing their ability to do other stuff instead.
The Tier Bonus Problem:
How does the loot system deal with the fact that some classes' tier bonuses are overpowered?
(Priest Tier 2 comes to mind.)
(In hardcore guilds people care quite a bit about their performance and will want to be the first to receive those bonuses. In more casual guilds, players of a class may stop showing up if they know someone else is getting all the tier items.)
Hunter loot is a bit more extreme in this regard. Where the upgrade path goes along the line of: Dungeon gear -> Full tier 1 -> Full tier 2 -> Full tier 3. If your hunters and priests are competent players, they will understand the situation. Obviously the player that received full tier 1 first, will not receive full tier 2 first. Nor will that person receive other exotic items first, such as weapons, trinkets, rings etc. With the understanding that going into BWL for example, 6 tier pieces are already reserved for them. Priests getting their hands on the Azuregos hat for example, would obviously fall behind as well. It is an extremely scarce item.
The Racial Bonus and Weapon Type Problem:
Sword of +1 Slicing drops. Rogue A is human and has a bonus to swords, Rogue B is not. How does the loot system handle that?
(Although this will probably be much less of a problem in classic now that DPS can be simmed so easily.)
An Alliance rogue rolling anything but Human does so with the understanding that they will be going dagger specialization. There are only so many weapon drops, and some of the weapon dropping are daggers. Sword human with Vis'kag + brutality blade may be the best DPS in tier 1, but dagger rogue with perdition blade + core hound tooth is better than a sword rogue with blue swords. The guild can't throw away epics, because the ideal geared sword rogue is better than the ideal geared dagger rogue, when ideally geared sword rogues takes months to get.
The Bad RNG Problem:
In vanilla with the large raid sizes, relative scarcity of items, and lack of tokens, it's very common for a few raid members to have one item slot they just can't get the drop for.
As an example, imagine a mage that just can't get a caster necklace to drop after farming Molten Core for months. Then, in BWL, a caster necklace with spirit drops that is a huge upgrade for the mage but a small upgrade for all the healers. How does the loot system handle this?
Give it to the healers.
The Wonky Itemization Problem:
The equivalence of items, especially jewelry with spirit or MP5, can be very hard to judge. Is a neck with 15 spirit a bigger upgrade for a shaman with a 9 spirit necklace or a priest with a 7 MP5 necklace? Or what about that mage from the Bad RNG problem that is still wearing a blue necklace with vastly lower intellect?
Because the value of those stats depends on the length of the fight, the other gear the person is wearing, and the other tier bonuses acquired, there's no single correct answer.
You're kicking the bucket down the road if you keep giving items to players, based on what item they are currently using. If you give the spirit neck to the shaman, the overall performance of the raid increases the most. But then a neck with more MP5 drops, which is now a bigger upgrade for the priest. Then you end up in a situation where the Shaman and Priest would like to swap necks.
The BoE / Legendary / PvP item Problem:
How does the loot system deal with BoEs and other novelty items?
(The biggest difference from retail is that many powerful PvP items dropped in PvE raids, as opposed to cosmetic mounts.)
BOE :Same as BOP
Legendary:
2H mace - Who cares? To a dedicated pvper who would be using it and has the highest attendance etc.
Tanking sword - To main tank
2H staff - To whomever will continue playing after Kel'Thuzad is dead
Pvp items: To players actively participating in PVP with the intent to eventually hit R14
The Alt Problem
One of the few things that's probably more problematic in retail, where a boss like Mythic Kil'Jaeden is significantly easier with two guardian druids, a blood death knight, a holy paladin, resto shaman, disc priest, resto druid, warlock, and as many rogues and preferably mages as you have after that. It might be an issue on 4 Horsemen where 6-8 tanks are helpful, but generally alts weren't as needed in vanilla.
And then there's two "Modifiers" that can affect every single other problem above.
Main > Alt
The only reason to deviate from this is if a guild member is swapping to tanking upon request. Then that person will probably show in on farm days to pick up tank gear. You would be pretty damn stupid to deny tank loot to a guild member abandoning their current main to start tanking. It's not really an issue in T1 and T2 content however, as most of the tank loot is exclusively tank loot.
The Upcoming Boss Modifier:
A modifier that pretty much affects every other problem above. If the loot system is set up to spread the wealth evenly, but on the guild's first Chromaggus kill an item drops that would give a priest their mana-return tier bonus for the upcoming 10+ minute Nefarian fight, is the guild going to change the loot system?
If a guild's loot system is to always give their main tank the best available, but the next progression fight requires five tanks and 2 of them are sorely undergeared, is the guild gonna change the loot system for that?
If the intent of the system is to distribute the loot evenly, then you have already failed at distributing loot. The number 1 rule in running a guild, is to never ever arbitrarily deviate from the set loot rule set in place. People tend to get grumpy if loot is mismanaged. If Chromaggus dropped an item which is really good for a player going on Nefarian, the system should have been set up in such a way as to award that piece to the player, before the piece dropped.
The Pain In The Butt Modifier:
How complicated is the system? How much time does it take to administer? How much arguing does it cause? How long does the raid have to stop to assign loot?
Probably 30-90 minute meeting a week between the ''loot council''.
Why would the raid ever stop to discuss loot during the raid. Just a bit above, you wrote about consumables. Which are ticking down 40 times per second, one second for each player per second the raid stops. Clear the raid and raise your grievances between the raids.
----------------------------------
The key is to find a group of people, that understand classic wow. I play a hunter on private server, and i understand that certain items which are extremely powerful on Rogues and Fury warriors will not be assigned to me in the top 10 on the list. Nearly regardless of how well i perform, how much i farm, how much i scout for world bosses and however many level 60 alt characters i bring to the raid. If i top damage meters, show up with all consumables plus flask, scout for world bosses 20 hours a week and manage to get a warrior and a priest to level 60 to tank and heal. I may get Drake Fang Talisman as the 6th to 8th person.
If your hunter is whining for melee loot (and not joking). Find a new hunter.