Yeah I believe it was mentioned somewhere that her cloud powers could be alien in origin but I don't think it was ever 100% confirmed & it could do with a bit of further explanation. You're right about the secondary characters in that the vast majority of them didn't have explanations for their powers but they didn't really get a lot of face time so while I wouldn't mind seeing explanations for any of them it's not hard to see why we didn't get them.
In the Ultimate Univers Geldoff/Proton's powers were pretty clearly explained so we could maybe assume his 616 counterpart received his powers in a similar fashion (via experimentation while he was still in his mothers womb)
The only other real character I think they could've explained a little more apart from Cloud 9 was Baron Von Blitzschlag . We know he was a ex Nazi villain/scientist but beyond that the origin of his powers was left pretty vague...Speaking of the Baron I think it would be pretty neat if James Robinson could sneak in a cameo for the good old baron in All New Invaders.