Go Team Reimu! If you win I'll make a donation to the Hakurei shrine, will subscribe to the bunbunmaru newspaper, bring some fine liquor for partying and bake a cake for Yukaris 17th birthday.
Reimu A (Reimu/Yukari) is, as always, the most powerful shot type in the game and the best general combatant. Even if the straight focus is somewhat limiting, it's just hands-down much more powerful than any other shot type except maybe the hard-to-use stone sign of Patchouli, and the ability to teleport from one edge to another is basically a get-out-of-death-or-forced-bombing-free card in the constant streams of aimed shots around stages 5 and 6.
That said, Suika's homing shot is weak, and Aya's shot type is the absolute worst shot in the game because you have to spend more time fighting with the direction your shot is facing than dodging bullets, and just to make that unforgivable, it's weak to boot!
Meanwhile, Alice has above-average power and having twice as many bombs is nothing to sneeze at, although it has the annoyance of its unfocused shot having a linear stream, while focused shot is a spread, which is the opposite of what you want.
Patchouli tends to take more strategic play, but wood sign is terribly powerful, and stone sign is extremely good whenever you can use it (like getting above Yuugi or Parsee), and the bomb is hugely powerful, but you have to plan to use it since it's so short-range. I do best with Marisa/Patchu, but I also plan ahead of time which spellcards I hate the most and will "bomb-out" those cards by charging the boss and bombing just before the first shots come out, and wood signing them the whole time. (You can normally take out almost the whole spellcard on a single bomb's time if done properly.)
Nitori is basically the exact same thing as Yukari, but weaker.
So basically, Reimu A and Marisa A and B are the only really good choices, and many people don't like having to swap signs for Marisa B, so it's not like there's a terrible difference in teams (although Marisa's is generally stronger), it's just A-type biased.