It's the little things that bug me the most about the game:
1+1 exotic limit is terrible design in a loot-based game.
Story missions give no item rewards at all once you're level 20.
Engrams decode into shit that's lower tier than the engram itself. I'm still wearing a L14 chest with no Light on it because every single blue engram I've decoded has given me a green chest.
Factions are all PVP-related, PVE only gets Vanguard. Vanguard legendary Titan gauntlets has bonuses for scout/sniper and AR/shotgun only. Like pulse and fusion rifles (what I use)? Sorry, you're fucked. As a double "fuck you" the boots have hand cannon and pulse rifle bonuses instead of allowing you to get a full suit that buffs your weapon of choice. Also, you get the stats they give you and that's it. With factions, you're able to choose the two stats you want by picking the correct faction. Granted, it's still not perfect because you may not find the gun mods you want on the armor that has the stats you want.
Exotic weapon bounties require both PVE and PVP to complete.
I've explored most/all of the ?? areas I came across while leveling and at most they have a dead ghost in them. Is there even a reward for collecting all the dead ghosts on a planet?
The level scaling gets really obnoxious after a while. Killing enemies in a patrol is no easier/faster than killing them in a hard mission. They just do less damage to you. At least they also drop level-scaled loot, but still... there should have been L20 patrols with greater mission rewards.
No idea wtf is up with events. Every time I come across one on my Titan I end up having to try to solo it because nobody else shows up. Doesn't matter if it's prime time, Saturday afternoon, etc. I've had better success with my Warlock while duoing with a friend, but even then events seem absurdly rare. If we see three in a night it's a goddamn miracle.