For me most definitively hottest item is independent cool-down on powers. Even if I play (or more to the point - I'm totally addicted) ME in any capacity for about 2 years (until last year I was completely unaware that ME3 was out... because it's Origin locked meh..), I've read multitude of threads and people demanded that since ME2 was out. Finally!
Changing specialization on the fly.
Looks interesting at first, but ... Here I prefer old ME approach, which forces you to adapt. Pick adequate team to complement you. I didn't liked what ME2 did when program cut access to full arsenal for non-Soldier - and small mod rectifying this was very welcome addition. Especially changing on the fly from Soldier to full Biotic or from full Engineer to full Biotic seems like vast overkill and it may be (Mordin-)Problematic. It has a potential to create insta-win setup(s).