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Much thanks to User:willydstyle for sparking this idea.

Game Mechanics

1. Stacking Saving Throws - an assassin with armor, field, and dodge saves, or a chaplain with terminator armor on top of his 4+ invulnerable.
2. Close Combat - Sure it was kind of cool that you worked out fights on a model-per-model basis... as long as you didn't have too many people fighting. If you had a big scrum it just made the game take too long. Plus, having extra attacks was more of a hindrance than a benefit, because of how the critical hit/fumble system worked, and having multiple sword-type weapons giving extra parries... made non-swords really redundant because of how CC was all-or-nothing. You either won and got hits, or lost and got hit, but never did both models hit each other.
3. Saving throw modifiers - I know that tons of people love them, but they really made non-terminator-non-invulnerable armor pretty worthless. Why take a regular space marine when a shuriken catapult reduced his save to a 5? A heavy bolter reduced the save to a 6... There was a reason why most space marine players I knew just took as many terminators as they possibly could.
4. Game Length - Ridiculously long games.
5. Sustained Fire Dice - Also known as Jam dice. Nothing like those terminators having to clear jams every other turn rather than actually killing something. So much for treating their weapons as holy objects to be maintained religiously!

Psychic

1. Endless Psychic Phase- With the Dark Millenium expansion this phase took up half the game easily, and I didn't like the fact that so much of the game hinged on one model. Often times it seemed like players assumed that everyone was going to come to the table with one max-level psyker, so often I wouldn't bring a psyker at all so my opponent wouldn't get enough cards to play his high-level power psyker.

Wargear

1. Redundant Options- Sure there was tons of neato stuff to give your guys... but nobody took power axes because swords gave you parries, why take autoguns when lasguns gave you a -1 saving throw modifier for the same points, etc.
2. Virus Outbreak - Some armies were totally immune (making the card worthless) and others were totally vulnerable (making the card an auto-win).
3. Vortex Grenades - Killed anything it touched (excepting models with a Dodge or Displacer Field). Kept wandering around, turn after turn.
4. Blind Grenades - Step 1: Have your ten man assault squad toss blind grenades. Step 2: Spend 10 minutes each turn figuring out how big they clouds are this turn and where they drift to.

Eldar

Solitaire: The Eldar Solitaire was a level 4 psyker and the Harlequin's Kiss could easily take down a Land Raider in one hit.

Space Marines

1. Terminator armor saves on 2d6
2. Cyclone Missile Launchers They tried to make a mechanic where the player had to choose between conserving ammo, and front-loading damage. This failed not only because front-loaded damage was much better because of first turn advantage, but because of math. Think Pi times radius squared, on a krack missile that had a 1/2" radius for each missile used in one go... 12" diameter krak missile shots...

Models

From the hump backed, grinning orks, to the "I jus' wanna hug!" carnifex, the models of second edition were mostly terrible. Not helped by the 'Eavy Metal team's choice of bright, cheerful colours and all green bases for the game of epic grimdark.