I see where you're coming from, G, and what you say makes perfect sense, and I agree with most of it. VenMax certainly doesn't exist in my Joeverse (as you probably guessed!), but the Swamp Rats do as normal human Cobra operatives; I just choose to ignore the venom serum part of things. (Never let a file card/theme you dislike stand in the way of a good figure, I say!). As for Sigma Six, it just ain't my thing. I'm fairly hardcore into realism, and S6 seems to be more futuristic/fantasy based than most of the 3 3/4" line, and as such holds no appeal for me. (Plus storage space in my house is at a premium thanks to other hobbies and my wife's Beanie babies, so the 3 3/4" stuff has priority).
You are absolutely correct on the good points of the new sculpt figs; much sharper detail, some great new characters and some classic remakes (new sculpt Lowlight quickly put paid to my '86 Lowlight's career!). Mixing new and old sculpts together does not bother me at all, 'cos good figures are good figures regardless, and I'll use 'em all.