Lighting rules. I've got a rogue, a ranger, and a stealthy wizard IMC. The wizard is eladrin and totally frustrated by the binary nature of even low-light vision. There is no way to "hide in shadows" against low-light, you have to use cover. I'm seriously considering halving the radius of all light sources and adding the dim corona from 3e. I think I'll keep the dim-to-low-light corona as a +50%, rather than doubling the whole thing, though.
V-shaped classes (now that I know what that means). A-shaped classes are okay, I guess, but I think the builds should be I-shaped, with a tertiary clearly below the secondary.
Attributes that go to 20 at 1st level or up to 28 later. I liked my humans at 3-18 with the other races having some variation. I don't really mind non-humans having no penalties, because those were often crappy for some good concepts. I think I'd cut the number of stat bonuses by one for every race (one for most, zero for humans). I'd also kill the +1 to all at 11th and 21st levels. Not replace with +1 to two, but eliminate them. I'd also be fine with +1 to one at 4th, 8th, etc. and +1 to two at 11th and 21st. I kinda like increasing stats, but even 3e gave too much.
Multiple attributes feeding defenses. I like 4e defenses over 3e saves. The multi-attribute defenses gives some strange results, though. In my group, the Wizard (high int) has a better Reflex defense than the Rogue and the Rogue (high cha) has a better Will defense than the Wizard. The Wizard also has a better AC than the Fighter (battlerager == chain armor). I appreciate not forcing everyone to need three specific stats, but the results are wonky.
The mechanics are too similar between the power sources. I'm not saying a wizard feels like a fighter, or anything. I just want the sources to feel more different -- almost different sub-games. I think it'd be great if switching from a martial PC to an arcane PC felt very different. The Warlord should play more like a Fighter than a Cleric -- not in terms of responsibility, just the mechanical feel. Maybe a standard power advancement by source, rather than universal. I have some ideas, but I wouldn't say I have a definite solution. I think Psionics looks to be appropriately unique, though. Hopefully, WotC doesn't start passing that mechanic around.
The economy. I've made my peace with it, to an extent, as being completely fanciful above 10th level or so. No one actually has that sort of money. It's only a meta-game way of saying a Holy Avenger is as rare and valuable as owning a kingdom and a heroic king might have to forfit his throne for the opportunity to wield one. Things like the cost of mounts and armor, though, are blemishes and I'd don't like base equipment priced by balance.
Which brings me to Balance. There are a variety of issues that can be laid at the altar of Pure Balance. Some of the pricing definitely falls there. Disappearing artifacts, likewise. And a host of really minor, but pervasive bits. This is where the "board game" or "video game" arguments hold a thimble-full of water. A feat that lets you use Wisdom to attack with a sword -- WTF?
Treasure parcels. I don't have an issue with them as basic guidance, but it's become clear that the intent was to have exactly those ten parcels handed out for the given level. Give me a list of twenty and let me pick ten. They should be roughly interchangeable. Also, the money should be assumed to be split up more, rather than truly parceled. To freakin' formulaic. Also, give me a random table for generating items. Maybe mine are the only groups that played this way, but I'd be more inclined to walk on a DM who hand-picked every item than one who randomized everything. Sure, picking one or two a level is fine, but not everything. I have decide what useless crap to add to adventures, now.
Only getting 1/5 return on disenchanting magic items. Considering I hate hand-picked items and I hate magic shops, my players really need a way to exchange their items. It's still better than 3e, though, that practically forced you to have a magic item trade.
Fill-in-the-blank module parcels. Doling out items is one of the things I like least about building my own adventures. If the module authors aren't going to handle that, what's the advantage of using them. Yes, it's still less time I need to invest than doing it from scratch, but I actually enjoy building the encounters and one of the selling points of 4e was that it made encounter building easier. So, 4e modules do the fun, easy stuff and leave the crap work to me. Even if I subscribed to the hand-picked treasure idea, I'd still rather see the parcels explicitly distributed with money in room 17, and a fill-in-the-blank item in room 8. The treasure table at the front of modules ticks me off everytime I see it. And, because the encounter information says (if I'm lucky), "Treasure: parcel 3," I find myself forgetting to hand out treasure with some regularity.
And, yes, I did just complain about treasure three times, twice regarding parcels. It annoys me that much.
Feats can't seem to decide whether they are for tweaking concepts or tangible bonuses. Multiclassing is a good example. I didn't mind it, initially, because it looked like a lot of feats just did little things to help you define your character -- like stealthy wizards, fighters knowing some rituals, or a +1 in very limited situations. A steady stream of substantive feats have rolled in, though. Personally, I like feats as minor perks and powers as substantive capabilities. I could deal with feats granting some noteworthy effects, but don't use the same pool to buy personality tweaks.
I'd also rename "multiclassing" to "dual classing" and "hybrid class" to "multiclass". Asthetics only, but it carries forward the same basic meaning as 1e had.
Over all, though, I do actually think the base system is probably the most solid edition, yet. I just think that some of the... presentation, for lack of a better word, leaves something to be desired.