1) A plot that isn't bathed in stupid and badass.
2) Gameplay that isn't boring and so heavily cover-based.
3) A nice trip to The Illusive Man's base and shoot him right in his damn head.
4) Remove the god damn Paragon/Renegade system already. Its stupid and limits choices. Or it would, if ME1/ME2 gave you much choice to begin with.
5)Companion banter like in Dragon Age. Seriously, just do this. It fleshes out the characters, makes it seem like they do more than just sit in their area and faff about. Its just delightful.
6) If your going to have a reaper posess a mook and shout taunts, make sure he has more than 4 and doesn't repeat them ALL THE FUCKING TIME.
7) Planet exploration. The planets from ME1 with the Hammerhead from ME2. And the planets are actually interesting.
8) More open levels. Or at least more levels that look open. ME2 suffered from a bad case of "corridor shooter". So did ME1, but at least the levels looked open and interesting.
9) Male Shepard has some actual emotions.
10) Companions that don't want to have hot sex with me after 3 conversations.
11) Your choices amount to more than just a few more/less emails.
12) Companions comment about things throughout missions, like in Dragon Age. Adds character and is amusing to listen to.
13) Certain missions that have special outcomes depending on which companions are following you, like in Dragon Age 2.
14) More hairstyles already!
15) Return to the more "sci-fi" soundtrack of ME1, rather than the "meh" orchestral stuff that was in 2.
16) No DRM(fat chance of that happening...)
17) If you must have "badass", put more of it into conversations. Example: In ME2 on the Citadel, the one reporter(who you can punch in the first game), paragon option when she asks you to respond about saving/killing the council. You just rip her apart with your words. And it is AWESOME.
18) No giant end-boss fight. It'll just look really, really silly(human reaper, space-ogre... lol)
19) Bring back the stats and upgrading of weapons/armor. It brings a sense of progression. In the beginning you couldn't do much, but at the end you were totally fucking awesome. Thats a great thing. Better than being awesome all the time, which gets boring and stale after a while. Just keep the upgrading restricted to the ship so you don't have to deal with a cluttered inventory.
20) Easter-eggs/hidden goodies are always fun and delightful. Can't hurt. If you include planet exploration, thats a great place to put them.
21) Bring back the elevators, just make them faster. They're better than the immersion-killing loading screens. And make the galaxy feel, well massive. And big. Again, just make them faster, which would mean optimizing the engine more. Or something.
22) More interesting classes. Vanguard and Infiltrator were fine, but every other class devolved into a cover-based shooter. With you sitting behind cover, shooting/casting powers at any enemy who pops their head up. And that is boring.
23) Don't bind every power to a single god damn cooldown. Give each power their own cooldown, and just make the cooldowns short.
24) Bring back the unlimited ammo please. And the overheating thing. Just allow us to cool our weapons off faster by holding what was reload. This also stops weapons which shouldn't have standard heat sinks(*cough*collectors*cough*) from having them and thus creating a tiny plot hole.
And yeah, those are my wishes. Or demands. Or hopes. Whatever you want to call them.