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Team Philosophy
Viewtiful Joe is a dedicated Point character, due to his high support needs and limited support value. He does best with a strong horizontal assist such as Bolts of Balthakk or Unibeam, and additionally benefits greatly from a vertical assist like Hidden Missiles or Jam Session. In general, Viewtiful Joe teams tend to take the form of Point/Support/Support due to his demanding needs of support.
Notable Supports
Doctor Strange
Doctor Strange is ViewJoe's single best friend for a variety of reasons. Joe can DHC to Strange for Palm loops off Superjump height Desperado. He can additionally hard tag strange and use his Shocking Pink move to OTG after he tags out, allowing Strange to go into palm loops from that. Furthermore, Joe's bomb can be used to activate Strange's counter super, leading to massive damage at the end of a Viewtiful Joe combo -- though you do need a second assist to enable the hard tag that leads into it (like Jam Session). Bolts gives Joe full combos off voom even from full screen with proper movement and zoning patterns.
Doctor Doom
Joe can use all three of Doom's assists well, but the standout by far is Hidden Missiles, which is excellent for both his combos and neutral. Joe can have a bit of the morrigan problem of people stalling him out at superjump height (though red vooms help with this). Missiles removes this counterplay, and additionally allows for uniquely damaging extensions that allow Joe to kill off a single touch. Finally, Joe is great at hard tagging to doom, and can utilize this to great effect.
Rocket Raccoon
Rocket is another excellent partner for Joe, who can use Log Trap and Spitfire both exceptionally well. Spitfire gives him excellent mixes with Red Hot Kick, whilst Log Trap lets him get full combos off grab into Desperado. Log is an excellent complement to Joe's zoning, with an extra 10 points of durability to add onto his vooms, and Mad Hopper and Rock n Roll are both great DHC options.
Morrigan
Joe is one of two characters in the game with a triple jump, making him nearly as good at abusing Dark Harmonizer as is Chun-Li. Joe can stall for ages up in the air, using Dark Harmonizer to accrue oodles of meter. In combination with either Doom Missiles or Jean Grey, this can be an extremely powerful strategy.