Terrible characters (excepting Ada, who somehow remained a good character throughout despite the game)
Useless characters (largely Hunnigan and Krauser)
Boring antagonists
Poor writing in general
Instances of cheap visual effects (cardboard cutout trees and N64 quality textures abound)
Sparse environments
Predictable and easily dispatched enemies (which was my biggest gripe initially - a travesty when we were promised enemies that were smarter than zombies. Regenerators remain the only exception)
Hit the obvious weak spot bosses
Awful QTEs
A currency/merchant system (fine in other games, doesn't belong in Resident Evil. There are better ways to accommodate an upgrade system)
Scenario drops the ball starting the second third of the game
Mind-bogglingly pedestrian puzzles
A focus on shooting/action (not bad by itself, but again, doesn't belong in Resident Evil anymore than it does in a Metal Gear or Castlevania game)
Ties to previous games incredibly poor
Forgettable soundtrack
Utter lack of tension or scares
Overly abundant ammunition and herbs
Game gets easier the longer it goes on
Unbelievably terribad typewriter placement (some immediately following the after-chapter save)
Escorting
Level design is severely hit or miss
Game overstays it's welcome a small bit
The camera, when aiming a weapon, is too close, forcing a majority of the player's left peripheral vision into Leon's head (it's fine when you are being approached from the right. But there remains a noticeable blind spot to the left that can result in unnecessary hits. Unless it's somehow canon that Leon is blind in his left eye and I just never knew it)
Stiff animation (except during cutscenes or when reloading)
I know someone will inevitably ask what I think it did right. So -
Actual aiming is smooth and functional. Precision hits are shockingly easy
Mercenaries is pretty damned good, taken as a pure shooter that isn't trying to be Resident Evil (I sometimes wish the main game had been canned and an entire Mercenaries game released instead)
Assignment Ada is pretty well done
While the level design is hit or miss, when it hits, it hits very well
Pacing is very likely perfect
Shooting is satisfying
Excellent weapon variety
Knife being tied to it's own button makes it the most useful it's ever been in the series (RE4 Wii Edition's homing knife attack makes it even more fun to use)
A handful of impressively set-up enemy encounters
Context sensitive death scenes
You can shoot Ashley, Luis, and the Merchant. Intentionally, even
New enemies are introduced very well