It doesn't sound like you have a problem with Heroscape game play only the "Battle of all time". The rules are so similar that other than OM's and spells there really is not much "porting" to do.
TREX's rules for combining them are simple and work great. Now you can add in all the fantasy creatures you want (Dragons and elves) and igore those pesky scifi units (agents and WW2 soldiers). I think you could skill use the deathwalkers as golums/clockwork and many fantasy systems have samurai.
If you want, you could use those rules and simple have all Heroscape units treated like colorless Creatures for SUMMON and COMMAND actions. Still use the OM's but most of the time they go on the PW unless it is destroyed or you have a good reason to switch to another unit (like siege). If you really wanted you could even choose a high value Heroscape hero and call it a Planeswalker, but draft about 200 points less in your army (marvel figures would be a good option here if you like). I would advise against allowing Heroscape unit be enchanted by cards - that is likely to break your game.