Wow! This is my first time really looking at this, and I'm rather astounded. Not only some really good, creative ideas, but actually there's a lot of map and unit ideas here that I've been planning out for some time, and thought I was the only one! Great minds think alike. Maybe I'll just send you my notes, if there's interest, since you're a lot further along on actually doing something than I am (my computer currently won't run the mod tools).
Let's see, comments and questions in specific on the GAR and Legions:
Is the Clone Medic's "Medical Treatment" basically similar to the stock Bothan regenerate buff?
I like that you did Ghost Company, I'd been planning them out too... the first unit with the faded orange markings, I assume that's for troopers like Waxer and Boil? And yeah, I think the rest of Ghost Company are just plain white phase-1 troopers, though I had considered putting really thin orange lines in just a couple of places.
I have to say, I don't like the bright green and bright white on the ARF Troopers, though aside from coloring I think they look great -- I'd recommend something in more of a muted olives and grays, like the picture from the Ryloth Lessu episode here: http://starwars.wikia.com/wiki/File:Recontrooper.jpg
Plus, the mouthpiece markings look weird in black and white, they make him look like a cartoon dog! I'd do a gray with lines in slightly darker gray.
Finally, I don't think Commander Ponds was part of Ghost Company, or even the 212th; I'm pretty sure he was part of Mace Windu's 187th (with the red-brown markings instead of purple like the rest of the 187th). I know the ARF Troopers at Lessu on Ryloth were part of the 187th -- Lightning Squadron. The ARF Troopers for the 212th (at Nabat) were actually Waxer and Boil, though they didn't wear the scout-type helmets worn by Lightning Squadron ARFs.
Since the ARF Troopers are focused on recon and information-gathering rather than attacking and offensive infiltration, I had planned to give them a limited Stealth, Recon Droids, Sniper Rifles, and Blaster Rifles. If you wanted them powered up a bit, you could give them a more powerful Blaster Rifle, certainly. The chaingun seems fine to me too, though, if you want to make them a more high-powered unit for their side -- chainguns are listed as typical weapons for ARF Troopers, after all! (ref: http://starwars.wikia.com/wiki/ARF_trooper
I like your 327th, too, looks good! I would agree with those who say they should all have kama, though. And pauldrons. If you're worried about differentiating the regular Sky Corps troopers from Commander Bly, you could just make the color of the kama different -- say, a lighter grayish-tan for the regular troops, and a darker brown-tan for Bly. It is canon for them to all have kama, though: "The troops of the 327th Star Corps were distinguished by striped yellow markings running the length of their armor and, as a result of Clone Marshal Commander Bly's ARC training, his troopers were allowed to don kamas and command pauldrons."
I'd also agree with those who said that the Clone Recon Trooper would make more sense with Stealth, rather than a Disguise Kit. The main reason the BX Commando Droids could have a disguise kit was because they were built to fit inside clone armor. Isn't a Recon Trooper basically the same thing as an ARC (Advanced Recon Commando) or an ARF (Advanced Recon Fighter)? Seems like the ARF is just an ARC who doesn't focus on assault combat as much.
The 21st Nova Galactic Marine BARC Trooper looks great, it's a really creative skin -- am I correct in assuming that's a creation of your own, or is that taken from something I haven't seen? Looks good, either way, I like the emphasis on the green visor lens.
And great work on the 187th, I really like them. The purple visor on the Jet Trooper is a nice touch. I seem to recall the 187th Clone Commander having more purple markings than you're showing here, though -- yes, it looks like there's purple on his kneecaps, the backs of his hands, and across the top of his chestplate, and a little on the mouthpiece of his helmet. (ref: http://starwars.wikia.com/wiki/File:187thLeader.jpg
Again, GREAT work! Looks awesome, I'll be installing it and trying it out later today.
(Ed. to add the chaingun bit for the ARFs, and to distinguish between the Lessu and Nabat ARFs)