Cars in Borderlands. I died more times in my car than out of it. You know something is wrong when someone is shooting at you and the first thing you do is stop and jump out because it's going to explode any second. The thing is, as you got stronger and your enemies got stronger, the cars stayed the same. Early game, they're okay. Late game, they're cardboard armored death traps.

Fire Emblem Awakening - More Cutscenes.

Splatoon - Change the map and game mode rotation.

Animal Crossing - More ways to earn money

In Gears 3, Dom would have had a greater moment to shine. Love you, bro.

The Legend of Dragoon: Fix the mistakes in the translation and change the voice actors for better ones. Do that and I have absolutely no complaints left for that game.

To be honest, I've always felt like he should have had more screentime, too.

Xenoblade Chronicles X - Change the party member mechanics completely. Make them all level at the same time (or at the very least give a Zero EXP option for the player character) and have the option to either switch party members on the fly, or at least have them within quick walking distance of each other. The party member leveling thing seriously bugs the hell out of me, especially considering they didn't do that in Chronicles, and there's like 15 party members. I'd probably like the game as much, if not moreso, than the original if it weren't for this.

Sonic Generations - The final boss sucks. It really does. The music is the only original music piece in the game and it blows, and the actual fight itself is boring as hell.

Most 3D Zeldas (expect Ocarina and Majora) - Speed up the beginning. SIGNIFCANTLY. It shouldn't over take an hour to get to the first dungeon. That's part of the reason I love the 2D ones so much and why ALBW was so refreshing, you got to the first dungeon within 10 minutes.

Fire Emblem Awakening and Fates: More anime cutscenes. They're all incredibly well done, if they did that in between all the chapters, my immersion would climb to a whole new level.

Again on FE: Awakening: I would change the last battle with Grima. It seemed to end too quickly. I won the final battle on Turn 3. I'd like it to be like the final battle in Fates, where even after you beat the 'final' boss, there's another one ready to face you right away.
I'd also like the extension chapters to be available before the final battle, so I can recruit Emmeryn earlier.

Shiek revealing herself as Zelda then immediately getting captured by Ganondorf in OOT
I really feel like Shiek should have been his own character. but, it was still cool just that scene kinda irks me a bit.

ICO HD: re-render the backgrounds showing the rest of the castle. The low poly backgrounds stick out like a sore thumb, otherwise the game is perfect.

Grim Fandango: Freezing barf puzzle was a step too far.

Windwaker: Add the missing dungeon. I didn't mind the fetch quest or long sailing, yet the end felt very rushed.

Dark souls: Add an option to turn off hostile invasions. Yes I log out of psn when the message appears, do not want.

You could always play on 360 and refuse to pay for Xbox Live Gold. Problem solved!