You're fast, Shawn
As I already mentioned in Spud's thread, the use of GI Joe parts (particularly the legs) is not favoured by all of us, due to the look of said legs. I personally don't have one favourite base figure and just try to find parts that resemble what I'm looking for as closely as possible.
I've also noticed male GI Joe figures are often taller than their SW counterparts, making them out of scale a bit. Doesn't really matter if you're making a tough alien biker or a taller Endor Commando, but just wanted to get that out.
The new VC45 Clone is definitely a top base figure to use for creating Clone customs. It's the new ROTS41, so to speak
I've never owned a Marvel Agent Helix before, but for female figures I tend to use (parts of) the GI Joe/Cobra ladies. I'm working on a female smuggler using a Marvel Universe Ms. Marvel too, which is pretty easy to customize as well. The articulation on that mold is not as good as on the Joe figures, but it works.
My 2 cents:
Male human bodies: for articulation research Joe parts, keep scale and overall look of the figure in mind. Clones: the new VC45 sculpt, great base figure to repaint, switch helmets, backpacks, belts, etc. Want to keep the Hasbro SW look intact? Stick to SW figures. Rebel crew, Bespin Luke make for great base figures to add details on. I've got this ultra cool Mando Neo Crusader from Ruprecht, which has the VTSC Bespin Luke as a base, with armour sculpted on it. Awesome use of that figure.
Jedi: well, SW Jedi figs, I guess, although TOR Jedi can be created from armoured Joe figs, like the reactive impact Duke and Ripcord and such.
Sith: again, these guys are often clothed like Jedi, but with TOR out now, you can again really benefit from armoured figures from other lines.
Mandalorians: I still use the standard Jango/Boba bodies, with limbs switched out and such, but try to make them look different enough. I feel Mandalorians wear similar style of armour during each Mandalorian "age".
These are just my thoughts on this subject and what works for me