I'll make you an offer - I'll work on adding all the mercs and you work on balancing them. ;-)
Well, I wouldn't make them kids. ;-) It won't make much sense timeline wise, but you can't have both, so people are going to have to decide whether they want the mercs to be realistic (age wise, not to mention all of them being on the island somehow :D) or want to use their favourites.
We could make 2 mods - one with just the mercs that could somehow be there (possibly with a little quest added to it that shows what reason they have to be there), and one with those plus everyone that couldn't possibly be there for those that don't care about the timeline.
Hey, we could add a time travel quest where you can get your favourite mercs from the future. We just need to make sure that future Ivan doesn't touch his younger self and destroys the universe. :D
I definitely agree about melee. I would love a pure melee/stealth merc to be a viable option. Stealthing JAF like Splinter Cell would be fun as hell. :-)
We also need more doctors. They are not as important as they were in JA2, but only one starting merc being good with medical (and even he isn't fantastic) is not enough.
If I remember correctly, all the details about the perks are in the JSON files, so modding them shouldn't be a problem.
Marksman needs to be split up (or rather added to it) into long-range and short-range (Sniper, SMG specialist, shotgun specialist,?anything else?). If we add explosive weapons, we need those as well. Other than that, I think you got it covered.
I also think that the perks should have a bit more of an effect, since they seem the only real reason to level up now. You should really feel how much more powerful the merc is in his field now and using a merc with a certain perk should make quite a difference to not having the perk.
Not sure whether that's possible, but I would also prefer the perks to be choosable to some extent. It wouldn't make much sense for Shadow to become a mechanic or explosives expert, but being able to choose between several perks that fit the character would be great. Just something to think about for the (probably far) future.