Can I at least bring in the new characters from each expansion without include the expansion they came from? Or would even just that screw up the flow/balance of the game?
Most characters will function fine using just the base game. I don't think there are any that get 'better', but there are a couple that get worse, or need tweaks (this is NOT a complete list)
*Cat Burglar (City) loses out on the extra City shops.
*Chivalric Knight/Dread Knight (Sacred Pool) So long as you allow them their starting Horses, nothing is really lost.
*Tavern Maid (City) is similar to the Knights above in that she starts with expansion-specific cards.
*Most of the characters from The Dragon expansion lose something due to the lack of Dragons/Dragon Lords, with Dragon Rider likely losing access to ALL abilities.