I know that for me, that is indeed the case. I love the interpersonal relationships and soap opera antics of Cobra a lot more than of the Joes.

Though personally I've never come across a chance to pick up a good run of Special Missions. I'd love to read it all, though, because I like to see small teams of Joes doing their thing.

Personally, I don't know why Devil's Due doesn't reprint all the Marvel stuff in trade paperback form. Marvel's reprint rights must have expired by now, and if Dark Horse can publish Marvel's old Star Wars comics, and Titan Books can publish Marvel's old Transformers comics, I don't see why Devil's Due wouldn't want to get the old Joe stuff out there. Unless, of course, they're afraid some old Marvel reprints would outsell and be more popular than their current offerings-- Which is probably true!

And regarding the discrepancies you bring up over the course of the run, that tends to happen in all comics when they're first being established. You have to be willing to live with a few continuity glitches early in the life of any comic book series while the characters and mythology are still being established. I don't really think much about it, myself.