Implementation: The way I would see this is that you can create squads of X men (subjective number). This would make it easier to hire/unhire and affect a squad of soldiers to a dropship rather than scrolling across the list of potential soldiers.
Jagged Alliance 2 allowed you to group your mercs into squads. Made management much easier. Not sure about the "leader" bonuses stuff. Maybe a "Leadership" stat (again, copied from JA2, though it was used differently in that game)?
2: Cryo weapons? Support Weapons?
Purpose: Those weapons could be use as lethal force but their main role is to support teammates or fill specific roles.
As you said, it's not much different than the flamethrower. Except for the TU-reduction aspect, which can already be done using flashbangs.
3: More non-combat items requiring to be used
Purpose: Allowing scouting and giving a nice range of combos with one handed weapons such as pistols.
JA2 and Silent Storm also have "sneaking" skills, IIRC. Neat idea, but would require a lot of work.
4: More Aliens
Purpose: longer mission, less Alien hunting across larger maps, more action, more epicness and more strategy.
The reinforcements idea is neat. The other stuff is kind of questionable. Certainly, there are strategy games were you can assign unit formations (Homeworld), but I'm not sure it's appropriate here. I guess it would be up to the AI scripters, but it sounds like a lot of work.
5: More armour
Purpose: While there is a nice selection of weapons, the armour selection is pretty limited, I would like to see heavier armour restricting movement for more protection or the total opposite.
Not sure if more stuff is needed. Anyway, it's something modders can do quite easily.
