After going through all of your comments and messages I've reverted back to the original game play. Trying to change on the fly threw the game out of balance. I recognize the issues you've raised are valid and need to be addressed, but they will best be done so with a new version or sequel that can be fully vetted and carefully balanced. Thank you again for all the great comments and messages, hopefully I can learn from them and improve my future games!
I've uploaded a v1.0.2 which incorporates much of your feedback. In particular the achievements that used to only affect heroes used on the level now affect all heroes. Additionally leveling heroes no longer costs gold and does not raise the recruiting cost, nor does increasing special abilities. To compensate the foes should now become a little bit tougher as your heroes level up. Let me know what you think. Note that previous saves will continue to reflect the cost of the heroes at the time of the save.
I've put up a new version to try to help those who were getting stuck with a "Please Wait..." message.
Thanks for all the feedback on the game play. I'll be looking at some options around the increasing cost of heroes after you level them and the achievements. Keep the input coming!