Will this work with the regular heroscape game?
Yes, it certainly will work with regular Heroscape, although some of the units have a high cost on them (Thanos is 360 pts). If you go to the official site (linked above), you can see a few of the army cards. The only difference I can tell so far is that the Marvel characters are not aligned with any of the Heroscape generals (Utgar, Jandar, etc.) so they won't be able to benefit from the Flagbearers' abilities.