There aren't any bonuses that carry over to the standard "epic" mode of playing. It would probably screw up multiplayer, and make balancing more difficult. Although we did discuss some easter eggs to unlock or such, I don't expect anything like that honestly, and there isn't anything like that in now.
The scenarios have 3 purposes in general, with not every scenario trying to reach each area:
1. Provide a tutorial, especially the Gifts of Kylorin one, and to a bit lesser extent Fall of Cuantine and the Grand Menagerie.
2. Tell a story about the leaders and other characters, expanded what's in their background info. Especially the 3 "paths" focusing on Decius, Falamar, and Auric.
3. Present some fun new twist to the main game. Hopefully some of these you might want to try again for it, or at least get an experience you won't get otherwise. Kael wanted each scenario to have something different, though some are more unique.