Keep the Firewalker, increase its health, make it the primary mode of mineral-gathering (quick, easy, doesn't interrupt the flow of missions), show health status in HUD. Maybe choose between the Mako (improved, preferably, also able to collect minerals) and Firewalker at beginning of the mission/assignment, with each having its own advantages.
Make two or three dimensions of morality (alien-friendliness, nice/jerk, hero/badass), and create certain thresholds for certain dialog options, to enforce some semblance of consistent character in Shepard (The racist SUDDENLY really cares about quarian rights??), with the opportunity to have plot developments and subtle choices change his/her outlook throughout the game.
Return to leveling system for persuasive dialog, but make it unaffected by morality. Role-playing games need to encourage role-playing. Have a persuade level, with a choice each level between particular persuasive techniques, one being Paragon, and one being Renegade (e.g. 1st level: Schmooze/Frighten, 2nd level: Charm/Intimidate, ... last level: Inspire/Terrorize, etc.), with the opportunity to get all of them, at the cost of spending twice as many points on the Persuade skill. In dialog, choose "Charm," opening up a new wheel with each option representing a level you've earned. Maybe a fifth level of a particular alignment is unlocked when all four of the initial options of that morality are chosen.
If thermal clips must be kept, make them advantageous. Make it like the first game, but when you're overheating, you can flip through your clips. If overpowered, make overheating quicker.
Provide incentive to switch cover. Grenades or other explosives are a good choice here. Also, blind fire in cover could be helpful, especially as a squad command.