So in other games players are stuck an alignment to gain a bonus but Marvel War of Heroes avoids that. Instead players can choose which cards they want in their deck without worrying about losing a buff. A lot of players though still have questions about which alignment is best and that's what this will address.
The main three alignments are Speed, Bruiser, and Tactics.
There are a couple reasons why speed is the best alignment at the moment, first and foremost being (Friendly Neighborhood) Spider-Man. As far as Ultra Rare cards go, Spider-Man is the best. The reason is he is the only Ultra Rare at this moment that has an attack boost to one alignment. This means that all speed cards get his boost and it is a high percentage boost because it is focused to only attack and only one realm. Other reasons that Speed is currently the best alignment is because many of the rewards from the first event such as Fox-Trot Nick Fury and Maria Hill are speed based and decent for their rarities. Finally, the referral card which is easy to come by is speed based.
I would consider tactics cards second best at the moment. Despite bruiser having two Ultra Rare, both of them are self buffs. This means that although they may have powerful cards, the deck as a whole is slightly weaker. Ultra Rare quality Iron Man is the second best card in the game at the moment offering a boost to attack and defense of tactics alignment.
Bruiser has to be the third best for a couple reasons. The first reason being that despite being the only alignment with two Ultra Rare cards it lacks the highest level buff to a specific alignment. Both Speed and Tactics have an Ultra Rare card that boosts the alignments attack or defense, but Wolverine is a boost to selfs atk/def and Hulk is a boost to selfs atk. The upside to Bruiser is that there were several Rare, SR, SSR Thor released onto the market making it a little easier to create a high level Bruiser deck than a high level tactics deck.
There are two of what I would call Sub Alignments, Hero or Villain
This only comes into play for activating special combos in cards. To gauge with sub alignment is better we need to look at skill boosts. Currently, Hero is FAR SUPERIOR to villain as a sub alignment. At the moment there are only three boosts to villains that I am aware of and all of the cards that receive the boosts are sub par.
I felt this was worth mentioning because when looking for speed/tactics/bruiser cards to supplement your deck, it should be important at this point in the game to look for heroes. Unless the combo skill you have doesn't require all five.
Of course in the future as new cards release this could change.