In no particular order:

1-Dr. Venom
Having another 'Mad Scientist' on Cobra would definately 'kick it up a notch'

2-Colonel Sharp
His involvement with the team as a liason for the govt. was always cool (and since Flint and I have need for him in our current dio-story, I just customized my own)

3-General Flagg
The original Flagg, 'nuff said

4-Major Juanita Hooper
Doesn't matter if it was the Baroness in disguise (which would be an added -ness factor), having a 'pencil pusher' to attempt to 'nip/tuck' the Joe teams finances is a plus

5-General Austin
Much like Colonel Sharp, having a 'brass' who stands up to 'The Jugglers' is a great thing

6-Dr. Vandemeer
Hey, Cobra's got scientists.....the Joes should too.

7-Dr. Burkhart
Same as above, besides, the more girls, the better!!

8-Billy
I know that some people are against a Billy figure, most likely because they're afraid that it's going to be 'uber-ninja' Billy, but a jeans/black t-shirt/eyepatch Billy would be an awesome addition to Cobra. I mean, come on, he's Cobra Commander's son!!! Besides, mine and Flint's Joeverse is really built on the 'family aspect'....no matter how twisted it might be in some cases.

9-Selena
Just always thought she was a great foil/friend for Scarlett with the whole 'Duke' thing.

10-Pythona
Cobra-La or not, this figure could kick some serious @$$. Having her as a consort to Cobra Commander would totally bring a new aspect of 'female rivalry' to the hierarchy of Cobra.

Honorable Mentions: Candy, Buck McCann, Honda Lou, Presidents/Heads of Countries.......I know I'm missing some here, they'll come to me.

As for the next 2 questions, I don't understand (and never have) why so many people MUST limit it to one or the other. For 25 years, I and my best friend have taken bits and pieces from both and re-worked it into a wholly believable Joeverse. Making a choice between this or that is just remedial. The basic principle of 'G.I. Joe' is that so many differences can come together and make something amazing......

__________________
Non illigitamus carborundum~Vos mos non effrego mihi

Coming soon: 'JoeSpecialOps'