For lane battlers where you mix sub-decks my favorite is Riftforce, especially once you add the expansion to increase the number of available factions. The factions are drafted and each player ends up with 4 factions. Cards from a given faction share the same power but have different strengths. This gives a good variety of abilities but since there are only 8 in a given game they are still easy to keep track of and plan for.
Tyrants of the Underdark, is a bit different but I like it a lot: a river-market style deckbuilder where the market deck is a mix of two themed decks. The current edition comes with 6 factions.
If you are open to coop/solo then Marvel Champions is somewhere halfway into this direction. Each hero comes with a small preset deck and you then customize this by picking cards from exactly one of the four aspects (factions) available in the game.