Well first of all, I approve of any change that takes opportunist away from snipers. That's a broken skill if there ever was one.
I do think that as many "no brainer" skills as you've taken away, you've added new ones. My list of no-brainer skills on your trees that didn't exist in the original: Lightning Reflexes/flush, Jetboots/auto threat assessment, sprinter/grenadier for assaults (it might be a question on another class), deep pockets/holo targeting, field medic/covering fire, almost literally every choice on the sniper tree (which granted was like that in the original, but its moreso here), rapid reaction/repair servos, opportunist/extra conditioning. If this seems harsh remember that the original had a lot of no-brainer choices too. As a general rule, if no one picked a skill in the original, don't put it next to a skill that people did pick.
Giving snipers battle scanner as their first ability is questionable. Its hard enough to level a squaddie sniper already, now their damage is only as good as a squaddie heavy? Which is OK, sure, but remember that all heavies can move and shoot, and also fire rockets. Also remember that in Impossible there is no enemy with 3 health, which means non-criting snipers can fail to kill a sectoid.
I dislike your changes to heavy even though they might not be exactly disbalanced. Close and personal with an LMG makes no sense either from a gameplay or logic perspective. You've also seriously nerfed demolitionist heavy, my favorite playstyle, by making all its skills unavailable until rank 4 and also requiring the loss of will to survive and HEAT ammo, both important heavy skills.
Finally, if you look at the old skills they never asked the player to choose between active and passive skills, which meant that all builds would have the same number of activated abilities. You don't have to follow this rule but should you should at least think about why they would do that.