The game is pretty mazelike overall. Myouren Temple is an entirely optional area that you can access before you get to Eientei, but don't need to go to until the very end of the game. The Forest of Magic is ridiculously huge, Youkai Mountain is filled with annoying caves, and the final dungeon is confusing to me even after I already know where to go.
Rarities to me feel like they're just Common and Rare, but Rare isn't so rare that you won't find a couple of them just by walking around normally. You probably won't get every puppet the first time through, but you should have a good idea where most of them are anyway.
Cost doesn't seem to matter that much, honestly. Kyouko and Keine were my MVPs my first game, and Murasa seemed about equal to Yorihime in usefulness my second. Kasen and Eirin both seem kind of bad to me too. More than stat totals, having good stats in the right places, as well as good types and abilities, seem more important.