One piece of criticism that I'd like to make: considering the new contacts system, I think they should be visible on the Intel screen as a category. Maybe I've missed them - only played a few hours this morning - but I can't find one's contacts listed anywhere in the menus, meaning I'll just have to remember where they are. It's not a problem in the beginning, but may turn out to be unfortunate in the long run.
Some of the choices between skills seem quite tough, but I'm surprised at how quickly I'm levelling up - in the aforementioned couple of hours I already reached level 5, a third of the maximum level. I assume level-ups will slow down quickly, but it still seems pretty sudden.
I really like how using marines is an alternative to using money in some of the missions, and how I can use story points to improve my chances or get new alternatives. Very cool!
Overall, seems a definite improvement so far, but the above are a few things that raised my eyebrows so far. I'll probably report something else later because constructive criticism is useful, but make no mistake, despite my overall tone being critical here, I am and remain a fan of this game.