First off, I searched for this topic and couldn't find it. I thought we'd discussed it before, but it must've been elsewhere.
Anyway, I like the RoC figures quite a bit, and since my Joe-verse does not follow the movie, simply because of the mish-mash of characters in my universe, I've finally figured out how to incorporate them into my Joe-verse with some harmony.
I actually like that most of the troop builders have been more MARS-themed, because that's what I felt Destro was lacking, having only the IGs.
Anyway, here they are:
The MARS Troopers and Officers: These guys are Destro's blue-shirt/green-shirt equivalent (gray-shirts, I guess?) While the IGs are his CGs, these guys are the grunts doing the day-to-day operations. After all, no matter how great an employer Destro is, nor how handpicked his troops are, there's still going to be a bottom at which they have to start. They're not quite the cannon fodder that blue-shirts are, and actually spend more time doing the menial tasks about Destro's residences and factories.
Vipers/Neo-Vipers: These guys, again, are like the Vipers of Cobra. They're not Vipers, but I haven't come up with a name for them. I'm thinking that Destro uses the evolution of tech to name his ranks, with Iron Grenadiers invoking the iron-age, so maybe these guys should be the Bronze Somethings? Not Bronze Grenadiers, maybe Bronze Sappers, or something like that. They're gray-shirts in full combat gear.
Elite Vipers: Haven't really worked them out yet. They're definitely Destro's, but I don't know where to classify them. Similar to Alley Vipers, maybe. I'm thinking they're guys in transition from gray-shirthood to IG status.
RoC Eels: I love these guys, but they aren't Eels to me. They're Undertow (Undertows? is it like deer for the plural or not?). They're Destro's frogmen and navy.
Ice Vipers: Now these guys are Cobra agents. I never really cared for the original Ice Viper (I thought his helmet was silly the way it fit on him), so these are a nice update. I'd thought about them being Destro's Snow Serpent equivalent, but they just don't fit his ostentatious-yet-functional uniform style. As modern Ice Vipers, they're great.
Now for the named baddies:
Destro: It's just another change of clothes for him. the man is a fashion horse, as evidenced by his various uniforms throughout the years. What're a few more?
Baroness and Storm Shadow: Same as Destro.
Zartan: Since we haven't really had a Zartan figure, there's no issue here. The figure we got just happens to be a figure of him in transition toward taking on the appearance of a Pit guard. Sort of like the Con Zartan as Hawk set, only skipping the first phase.
Cobra Commander: I always assumed CC's face was puke-tastic (mainly because of the cartoon ep where he was eating and Destro walked in, averted his eyes and said something like, "Commander, please... your face..." This is just his head gear he wears while tooling around Cobra Island and not trying to inspire the men. The helmet and mask have to get a funk to them after a while and require cleaning. This is a special piece of gear Professor Rex made for him to help treat the damage to his face and slowly reconstruct it. How does Rex do this? ...
Rex: Not CC. I never liked Mindbender being the generic mad scientist, so Rex fits in great (as will Dr. Venom when he finally comes out. Thanks, MC!). Mindbender is the psych specialist for Cobra and that's it. Rex (Professor Rex, just because I don't want a bazillion Dr.s running around Cobra, plus, it has a ring to it, for some reason

) is a geneticist specializing in genetic manipulation and gene therapy. His reason for working for Cobra is purely selfish; they promised him the funding he couldn't get elsewhere. His main reason for such diligent research is to find a way to arrest the rare disease he has, causing him severe respiratory issues and disfigurement, thus the head gear.
The Joes:
I won't do a line by line for these guys, but basically Snake Eyes is always SE, no matter how you slice it. He just has changes of uniform. Most of the others fit in fine either as the character they bare the name of (such as Heavy Duty), or as new characters (Breaker, Sgt Stone, Ripcord and Armor Duke), or as greenshirts (Desert Duke).
The RA suits are simply Sigma Suits, as Sigma 6 is alive and well in my Joe-verse. However, instead of it being the sum-total of Joe, it is a rotating group of Joes and allies, selected for the specialties required by each mission. When a situation is so hot that even GI Joe isn't secretive/discreet enough, that's when S6 is activated. It has full deniability since it is not comprised of strictly US military, as the main Joe unit is. While foreign troops may assist GI Joe, they do so under their own country's colors, as the Joes do. When S6 is activated, there are no origin countries acknowledged, and no colors worn.
So, how does RoC fit in your verse?