After seeing 10 billion perfect review scores for Uncharted 2 I had to try it out. When I played the first hour I was like how the F is this game a perfect game because I kept dieing from platforming. I used to hate the platforming mechanics a ton. Then finally after getting through the painful bits I got to the 3rd person shooter and stealth part. Safe to say it is one of my favorite games of this generation and the reviews actually surprised me. And I do actually like the platforming now. Contrast that with FFXIII the reviews surprised me because it was rated so high, but it was not my cup of tea.

Auto Health regeneration in every single FPS since HALO.

What's worst is that they just don't do it as well as Halo. I could dig in Halo that it was my shield regenerating, but when it ran out I took real damage. Felt like I was a Protoss.

All the imitators just give you a health bar (or worse, some red frame on the screen) that just magically goes back to perfect condition if you take cover for three seconds. That and the goal-indicator with distance measure and the ONLY TWO WEAPONS AT A TIME convention has been ruining shooters for me for years now.

The whole Assassins Creed Series, the crazy movement in a direction you totally did not go to fucking up a mission or killing you, or even up to about the top to synchronize and jump off and die....

I agree, just not about the almost part. I gave up on Skyward sword after starting it back up 3 times. The sword control was just too much hit and miss. Reacting on the back swing instead of  the actual motion and doing the opposite 20% of the time. Stabbing was even worse with a 60% failure to respond rate.
It wasn't the only thing that ruined it though, together with the unskippable cutscenes you have to sit through again after a motion control failure, constant interuptions by Fi, empty overworld and going back to the same environments I had enough.

Having to collect stuff before I can end the game. For example, in Metroid Prime where you have to collect 12 Chozo Artifacts before you can enter the final area. The same happened with Metroid Prime 2 just that this time you have to collect some keys or whatever. This is also the reason why I didn't liked the Triforce quest in Wind Waker. If I want to find stuff I want to do it myself, I don't want the game to force it upon me.

That said, this stuff don't come close to ruin the games for me. All 3 are still my favorites games of all time. I mentioned them because I honestly can't think of a game mechanic that I hated so much that I couldn't finish the game.

Exactly. An other game that in my opinion does this well is Deus EX Human Revolution, but all the others are trash.

I strongly urge you to try Resistance 3.  It has health packs and a weapon wheel to avoid the 2 weapon convention.  It also has whacky weapons that upgrade like Ratchet.  That's why it's actually my favorite FPS of all time and stands head and shoulders above everything else on the 7th gen for me.  Half-Life 2 and Resistance 3 are my favorite FPS games in large part due to these conventions being ignored in a contemporary shooter.  It's nice to have a perfect blend of old and new and it's why I can't wait for Half-Life 3

Too bad Resistance 2 was as derivative as it could get. It almost killed the franchise, but Insomniac learned from the mistakes.

The required sneakiness in in Dishonored. it just ruined the whole experience for me as i don't have the patience for one kill at a time.