I'll try and go through your list and give you some answers and the general direction SM2 is going in.
There should be an option to downsize the UI in the settings. The galaxy map is implemented the way it is to accommadate specific gameplay features that are not yet implemented.
You can customize most of the marines that is not the Commander/player, excluding stats like Aggression. You can still change the name, portrait, and gear of each marine (according to their class).
You have a few questions about the gameplay that make me unsure how to answer you. You can play 95% of the game purely with the mouse, I believe the only functionalities that requires the keyboard is entering marine names, panning the camera, and issuing Delhi space strikes. Panning the camera can mostly be accomplished via cycling between marines and the camera orbit buttons on the bottom right, although that's clearly not the exact same functionality.
Three active skills is a game design constraint because there are other options each marine has that they didn't have in SM1, specifically door opening triggers and a larger pool of abilities each marine can acquire. Between class weapon effects, head/body targeting, and the potential pool of abilities, there are far more options a SM2 marine has than a SM1 marine did.
Quite a few people have expressed a desire for the full squad portrait on the tactical field and is something I am reworking at the moment.
I am not sure if there is an issue with your download/install, because there are quite a few tooltips implemented, including how to open doors (of you mouse over them), so possibly you should reinstall the game?