I cleared naxx 40 on my priest back than. Outside of all the main points people mentioned like controlling a guild of 50+ raiders , having the right classes , being undergeared , not understanding the game , not having any info sources outside of you wiping , disconnects and ques being a problem.
I can do a quick breakdown of why bosses were hard , if you combine all those factors , you would get the instance 0.01% cleared.
Spider wing 3/10 - Having a guild cappable of getting to naxx 40 with some gear and spending some time would gurantee this wing being cleared.
Anub
Required hunters who could play and kite , pretty killable for guilds who downed bosses in AQ up to twins.
Grand Widow Faerlina.
Trash to her took 30mins. She did pretty heavy aoe damage. Tricky part here was she enraged one shotting the tank , a priest had to mind control and a suicide an add into her to dispel it. Mind control had many break checks back than , like range , shadow resistance , taking damage , spell hit ( part of resistances ).
Maexxena
Easy fight , people had to learn to free people from X disable mechanic here. Also she stunned the whole raid for 6sec, basically since your MT couldnt dodge or parry in the stun , you had to pray he survived.
Abomination Wing - 10/10
Patchwerk 11/10 - Nobody knew what was going on for weeks. People avoided him like the plague. At some point people figured it out , wiped 1312312 times and killed him. First kills actually involved people kiting him for hours in a certain spot at the start of the spider wing. Later on blizzard added a poison spit that 2 shotted if there wasn't anyone in melee range.
Grobbolous - 3/10
This boss introduced the boss drops cancer on the ground , tank has to move it , so do the melee , + adds spawning.
Gluth - 4/10
Introduced the aoe adds before they reach boss mechanic. Much easier if you had dwarf priests as alliance.
Thaddius 14/10
Introduced the +/- mechanic. If anyone died and didn't give the bonus damage you wiped to enrage. If anyone went into the wrong camp it was a wipe. No easymod mods back than , remember that!
Death Knight Wing 10/10
Instructor Razuvious Impossible/10 if u didn't have good priests. Thats it. 1/10 otherwise.
Gothik the Harvester. 15/10
Personally i consider this to be the hardest boss in vanilla. It required insane cordination CC wise , DPS wise , on both sides. And by insane cordination , i mean insane cordination for that time. It had to be perfect for every single wave or it was a wipe. Much fucking harder than the 4HM.
The four horse-man: 8x 4/8 tier 3 tanks / 10. If your guild was cappable of killing gothik , you surely had the skill to kill 4hm, except the fact that it required 8 fucking tanks with 4/8 t3 , because a resisted taunt was a wipe. From here you can imagine the realm transfers ( just introduced ) and guilds poaching , guilds breaking up because of losing their main tanks etc. On top of that the encounter required some brains.
Plague wing Cancer / 10
Noth the plaguebringer 4/10
A very generic fight for modern standards , adds dispels , small dps check.
Heigan the Unclean 6/10
It came down to the point that if 25 or more people in the raid could do the "dance" ( was much harder and faster than naxx 25 ). You could kill him.
Gauntlet before Heigan 10/10.
It took 30 fucking minutes , it was hard , you could wipe , made heigan 15 times harder since you had 3-4 tries max per night. And most people required tries to learn the dancing part of the encounter.
Loatheb 6 hours a day farming ghost mushrooms in scarlet monastery graveyard / 10
Pretty much that , it required a strict rotation of shadowpots/bandages/healthstones. Farming Shadowpots took literally 6hours. Also healers had 1 heal per minute, had to use it on the maintank , so rotations were introduced ( there was an addon later on that showed who already used his heal , but it wwasnt very relevant when it showed up ). So 40 people had not to screw up their consumables rotation for 6mins , also healers couldnt screw up , also tank had to get good rng on avoidance and ON TOP OF THAT , it was a very tight DPS race. Which meant world buffs helped alot. So you really had 1 good try per night or 3 days depending on zul'gurub/onyxia buffs. The stars had to align to kill him.
Sapphirion 6/10
Introduced alot of new mechanics like the moving blizzard , the hide behind LOS to avoid one shot etc. The main problem with him was the fact that even if u were top in the world guild progress wise you needed to borrow frost runes ( you looted them from naxx from the walls around bosses ) to craft the epic frost resistance gear. So you needed good diplomacy with lesser ranked guilds , which probably already hated you since being the top guild on realms mattered back than( also you probably stole their best geared and most reliable players). Also you needed 1 priest in each group because of prayer of healing.
KT - 11/10
You needed dps , guardians under 40% had the most retarded snow ball mechanic , annoying dps race check phase 1 which lasted 5 mins every try. A lot of "one shot" mechanics , melee's had to interrupt every cast he did , alot of raid damage , burnt people's mana by 50%. Main tank could get oneshot if melee's failed. Required fully flasked of the titans raid. World buffs were almost a must.
Combine all those retarded factors with the fact that people didn't have any information or knew how to play and had to manage twice as big guilds and you can get the picture i hope.
edit:Oh yeah i completely forgot about thaddius being unplayable , so we had to do the raids at 2 am. It didn't help that our realm was the number 1 on the progress ranking ( meaining most guilds with best progress or crap like that )