I just read the IGN feature on what Mass Effect 3 should have and it got me to thinking about my own list...
1) Compromise
Mass Effect 1 had like 15 types of each gun and then 10 levels of each (Raptor V, VI, VIII, etc.). It had like 15 types of armor and then 10 levels of each (Colossus V, VI, VIII, etc.).
Mass Effect 2, by comparison, has like 4 types of each gun and only one level of each. It has like four or five types of armor, but most people just use the default and screw around with the color scheme.
Mass Effect 3 should compromise. It should take a cue from the first game by bringing back all the types of guns and armor as well as take a cue from the second game by having you continually upgrade those guns and armor instead of having multiple levels of each.
2) Better Action
All the combat in Mass Effect 2 took place in small areas. Combat in Mass Effect 3 should take place in bigger areas that give you tons of options as to how you want to gameplan.
For Red Dead Redemption players, a great example is the mission at Tumbleweed where you have to storm the mansion. You've got a long distance to cover and there are tons of ways to get where you want to go. You can take cover in houses, on the road, and then as you get closer to the mansion, you can flank left, center or right. It's so much fun running from cover to cover, trying not to get hit by incoming fire as you dash from side to side.
3) An Antagonist
Not having a main bad guy in Mass Effect 2 was huge. Not having a main bad guy for each mission was even bigger.
There is something about the anticipation of fighting someone with a reputation that gives everything a sense of urgency. In Mass Effect 1, you read about Liara's mom causing shit at Noveria, you go to Noveria and hear even more about it, you go to the laboratory and hear even more about it, and before you know it, you're itching to fight this bitch. What you're doing appears to have a purpose.
On the contrary, in Mass Effect 2, you keep hearing about the Collectors, but you rarely do anything that has to do with them. So the urgency disappears. The game feels like a game of side missions.
In Mass Effect 3, establish an antagonist or two right off the bad. Keep us updated on what that antagonist is doing. Make sure everything we do has to do with that antagonist. It will make the story infinitely more engaging.