Rather than a larger change in the game design for 3.5/4 it would seem more likely to have a rules refresh and cleanup of language, harmonising some effects and triggers and incorporating the errata. Some of the keywords need some modernising and with expanded rosters a bit of review as a functioning unit.
Essentially, more a soft relaunch than more extensive change to underlying systems. Including of all the cards as Faction packs would probably be required to satisfy playerbase though.
I do think that the Henchman - Enforcer - Minion is probably the only thing I think needs a larger rethink. Maybe higher HP than present but same or lower defenses, so they're less easy to just delete with focused attacks from beater of choice.