After playing around a little with shot types, I think this is how they stack up against each other. Any crackpot information is my fault only.
Highest
SanaeB focused
ReimuA focused, point-blank
SanaeA focused
ReimuB focused
ReimuB unfocused
MarisaA focused, MarisaB focused
SanaeA unfocused
MarisaB unfocused
ReimuA unfocused
SanaeB unfocused, ReimuA focused, MarisaA unfocused
Lowest
ReimuA (unfocused: homing amulets, focused: actual shotgun) does some of the game's best damage at point-blank range, but it's tough to get both shots to hit moving targets. The non-shotgun wave effect has full-screen range horizontally, but does minimum damage (though the minimum in this game isn't all that bad). The unfocused shot is actually stronger than the focused shot when not at point-blank range, though it's a significant step down. The homing here is the best in the game.
ReimuB (unfocused: homing lasers, focused: persuasion needles) is on the highest damage tier, both focused and unfocused. Its major problem is a lack of range. The unfocused homing is a bit odd but it does just fine with one target.
MarisaA (unfocused: fire bombs, focused: language helix) seems like the worst shot type in the game. Master Spark is very likely the worst bomb in the game for almost all occasions, and the damage output from both of the shots in this type is mediocre at best. The splash damage from the unfocused shot is great but not enough of the shots hit at once for it to be a good idea.
MarisaB (unfocused: echoing shots, focused: laser triangle) doesn't do anything that every other shot type bar MarisaA does better. The lack of range on the focused shot really kills it.
SanaeA (unfocused: snake shot, focused: water streams) does surprisingly decent damage unfocused (though you wouldn't actively want to use it against bosses) and slightly above-average damage focused. Both shots have better range than ReimuB.
SanaeB (unfocused: leaf blow, focused: green gusts) does damage comparable with ReimuA shotgun but has much better range, making it the strongest shot type in the game IMO. The unfocused shot is better left unmentioned.
Basically, don't use Marisa except to get the unique spell at the end of Lap 2. Pick your favorite from the rest. I think I overrated ReimuA on my first go-round.