1. Keep the weapon inventory from ME2, add the upgrade system from ME1. Ditto with armour. Make more of each.
2. Do not make persuade/intimadate based soley on morality. It makes no sense. Something more like Dragon Age, where you could upgrade speaking skill and bolster it with personal stats would be better.
3. Remove the stupid shield system blocking all biotic and tech powers from doing anything. Make it more relevant, eg. barriers stop biotics, shields stop tech powers, not everything stops everything.
4. Keep biotic charge. People who claim the game is generic 3rd person shooter have no imagination. Playing a vanguard? Get in the enemies face. Playing an infiltrator? Take shotgun speciality and use cloak to flank enemies. You get the picture.
5. Get rid of the hacking mini-games. Please. If you must keep something, make it more believable, eg. let Tali break the safe while you do something else.
6. Less generic missions. I loved the missions in ME2 which required less/no fighting, such as Samara's loyalty.
7. Less companions. ME1's number was great, talking to them all after each mission was pleasant. In ME2, when you had about 10, it became a chore. Also, no copy & paste 'loyalty' system. It got annoying. Also, give them some relationships between them. A romance between 2 other crew members could be fun to resolve. Do you steal one and earn the wrath of the other? Do you tell them romance is forbidden on the ship? So many possibilities...
8. Please give companions reasonable outfits. Jack, wandering around in a vacuum wearing only cargo pants, boots, a breather and belts is just stupid. Especially when people are shooting at your unguarded skin.
9. I liked Firewalker. Return some level of Mako sections, with this vehicle. Only make it slightly more resiliant to the mysterious homing bullets enemies seem to possess. When it takes (very literally) 1 minute of constant shooting to take down an enemy (on insanity) and they can return the favour in 3 seconds, the only real combat strategy was to hide behind a wall and sent out homing missiles. This is not fun.
10. Heat sinks. Please bioware. You claim they are universal, yet you can run out with one gun and still have some in the other. Let them cool down, ME1 style. When they overheat, you replace them, ME2 style. You can carry 30, they can go into any gun. Easy
Hmm... so many complaints... but I love Mass Effect so much!