Am I able to mix and match the team villians? or should they remain seperate?
Mix and match!!!
Only mix. Do not match!
Some of the original cards have special interactions with Nemesis cards and/or Device cards. Mix-and-match can impact how effective those are. Nothing wrong with throttling them down a little bit if you choose though.
For reference, most of the original Vengeance decks had 5 Nemesis cards. I know Baron Blade had cards that interacted with Nemesis cards, not sure about the rest (could have sworn someone else did too...). Some did it indirectly by affecting all Villain targets in some way. I think 3? of them had Devices (Baron Blade, Friction, Ermine)? BB had more Devices and more cards that interacted with Devices than the rest. I don't have my Vengeance on-hand atm.
None of the Villains decks have Device cards, but some have Nemesis cards:
Plague Rat: 0
The Operative: 3
Sergeant Steel: 0
Miss Information: 4
La Capitan: 0
Greazer: 3
Citizens Hammer and Anvil: 0
Bugbear: 3
Biomancer: 0
Ambuscade: 5
Also, Plague Rat, Sergeant Steel, and Biomancer have pleanty of minions without Nemesis cards.
On a related note about mixing, playing the Festival environment with Vengeance/Nemesis could result in a lot of counting and fiddling. Personally, I think my regular group would prefer to only play it with normal villains, but some people don't mind the overhead as much. It would be a really unusual game.
Yeah, MMFFCC is one of the more fiddly environments.
In all my playtesting I only played a few games that were Villains only, I did that to test difficulty and interaction, and really it works as intended, that mixing Villains with Vengeance makes for a better game than keeping them seperate.