Absolutely! Everything in Dice Masters is made to be completely playable with other sets.
There are a few very minor terminology differences between sets:
* "Sidekicks" in YGO/Comics = "NPCs" in D&D
* "Character" (comics) = "Monster" (YGO) = "Creature" (D&D)
* "Summon" (YGO) = "Field" (Everything else)
* The Villain affiliation is considered to be the same affiliation, whether it is the Hydra logo for Marvel or the stylized "V" for DC/TMNT
* "Good/Evil/Neutral" are alignments, not affiliations, and (currently) only exist in D&D.
Please feel free to ask any other questions you may have!
Thanks a lot for your help!