Correct me if I'm wrong, but isn't the comic supposed to take place right after the first movie? If that's the case, Peter and Dana would be dating for at least some amount of time (however unspecified). If that's the case, perhaps the comic will show the relationship evolve, then break down.
After all, the RGB episodes were only 22 minutes each, and were action pieces targeted towards the Saturday morning cartoon crowd. They were going to focus more on ghost busting, not character development elements as a romance or dealing with a break-up.
As for GB2, I would like to see some elements of it added to the comic (Vigo, Oscar, Janosz, mood slime, Slime Blowers) since I would consider it more of the “official” events, but at the same time, I don't think four out of work Ghostbusters would make for a very interesting comic. Perhaps cheat and revise the history just a little bit.
All in all, though, I'm looking forward to this comic.