Actually, I'm doing fine now in Commander. Once I got some more soldiers, the game seemed to let up on me a bit and I got enough people healed up to assault the Assassin's HQ. The Avatar Project got to its timer but I had a covert to bring that down.
Now I've gotten the Warden armor and more area feeding me cash. I've got the plasma weapons research about half done, though I don't think I'll have the supplies to get everyone new weapons until next month. The Assassin's shotgun is death incarnate!
The new 'ability points' thing is sure interesting. Each character earns ability points as they advance and do good things (like flanking enemies). These points can be spent to buy skills you did not pick on promotion, which can be incredibly handy. Each soldier also gets a few random skills from other classes that they can pick, though they cost more. If the soldier doesn't have enough AP to buy the skill, there is also a common pool of points to draw from. Now that I've actually managed to build the room that allows this training, it's made my soldiers a good bit more powerful! (Halo Targeting and Heavy Ordinance for all grenadiers! Deadeye and Lightning Hands for all sharpshooters!)
Edit: Also, there's a new option that adds extra turns in the turn-limited missions. Enough extra turns, by the sound of it, that you don't have to rush to the target though not so many that you can just sit there after each battle and wait for skills with 4-turn cooldowns to recycle.