Isn't Tunnel Rat based on Larry Hama, who wrote the original Joe comic?
I think Snake Eyes was kind of like the superhero of the team, in sort of a Batman-like trained to the peak of human potential kind of way. And his backstory kind of dominated the Joe comic over time (literally, Cobra Commander, Storm Shadow, Firefly, Zartan, and Stalker all figured into his backstory, and his romance with Scarlett also played a big part in major story arcs). When ninjas got popular in the late 80s, early 90s, there weren't any turtle Joes, but the ninjas were right there, so then he took an even bigger role (so much so that some of the comics had "Snake Eyes" printed more prominently than "GI Joe" on the cover of the GI Joe comic).
Beyond that, it's hard to say. I liked Lifeline, Mainframe, and Dial-Tone, myself.