I agree it feels like a bit of a heavy work load sometimes to get to the daily cap with a smaller guild, when there's only one and a half group ready for random heroics. Especially now that the most active ones got to 85 and aren't questing anymore (which they already nerfed anyways). So it's all down to how many random heroics you can do with a guild group in one day.
I don't feel like the guild (achievement) rewards are necessarily unfair to smaller guilds. Some seem balanced in terms of benefit of the reward vs. guild size. For instance, the reward from "Stay Classy" (which is 8th guild tab) clearly is much more needed in a bigger guild. As is the cauldron thingy. Don't really need that in a casual raiding guild in my opinion.
And some items I don't really have any interest in. But sure the companions and mounts are much easier to get in a bigger guild, and I wouldn't mind those, being a collector (same goes for the cooking recipes ). It did concern me whether I could get those at any point due to our guild pretty much disbanding and only a small core regrouping elsewhere. But I don't have time to get into a proper big guild at the moment, so I'm "stuck" where I am now (I wouldn't be in the guild if it weren't for the people in it though, so it'd also be stupid to leave them just for better guild perk).
As much as I hate the guild reputation cap (wouldn't mind at all if it was uncapped so quest rep wouldn't have gone to waste - and let those farm to exalted in a day that wish so, doesn't mean everyone will get there as fast), I think maybe it would be better to have a weekly guild experience cap rather than daily. Bigger guilds would still have easier time getting the cap, but then smaller guilds would be get less penalty for having major activity towards the weekends, since in a smaller guild there might not be many who can play all the time.
One thing I was thinking about was that the guild reputation (maybe exp) gained should somehow scale based on guild size. In a way logical - if a guild has 1000 members no one's going to notice yet another guy who does a quest, where as in a 10-man guild one person is 10% of the whole guild, so it's much more reputation worthy to complete that one quest in that guild. Something along those lines, anyways.
edit: I'm still surprised though that people from bigger guilds aren't complaining and crying over how easy it is to get to the cap and smaller guilds should really have a hard, if not impossible, time with it.
Actually, that would really be impacted by size. It's at the moment realllllly difficult to do enough heroics in a day to get the cap when you have perhaps 6-8 eligible characters and others are still leveling. And getting at least 4 people that aren't only dps online at the same time with enough time and interest to get a heroic dungeon will really be difficult in a smaller guild, so at least you get SOME experience from people who are questing. Mainly talking about heroic dungeons because you can't raid every night and I haven't gotten there yet with our guild. And there's division between pvp and pve, some do both, others do either-or.
I guess it also comes down to the point whether or not small guilds need to level as fast as big guilds, but then again why should we be less "experienced" if we want to only gather people we know already and have fun with semi-retired ex-hardcore raiders.