by Braithwhite
There are a couple of minor changes that were made to hero decks in the 2nd edition.The ones that I remember off the top of my head are that:
1. Tempest's "into the stratosphere" was modified slightly in 2nd edition to exclude indestructible cards (in 1st edition, there's nothing on the card prohibiting usage against, say, Spite's drugs)
2. End of days was modified in 2nd edition so that cards with the "relic" keyword were spared...and Fanatic's equipment gained the Relic Keyword. In the expansion, Apostate (her nemesis) has similar relics and a card that mimics end of days.
3. Visionary's Wrest the mind was clarified and re-written slightly so that it couldn't be used on character cards (preventing some potential infinite damage loops and making the Villain card hit themself.)
All of these changes can be found at the GtG rules forums, and spiff has them all collected at http://www.spiffworld.com/sotm/.
Basically, if you are willing to keep the updates handy and do some homework, it shouldn't be a problem.
Or just wing it and have a great time debating the rules and figuring out what works for you!