Just a (belated!) update: I am in fact still working on playing through this, although I switched to a regular, non-fixed party run. It's slow going, but it's up to 14F (final being 20F) now. Been pretty busy, both with real life and with other games ;)
My actual endgame skillpoint distribution is going to be all over the place (since there are some characters I no longer use, and thus won't give skill points to anymore, resulting in inequal distribution). Luckily, I'll have a means of figuring out the total number of skill points earned throughout the course of the game: I can write down all characters' skill levels, load a clean NG+ save file that carries nothing over (so all it has is all characters unlocked at level 1 and no skill points allocated), use a memory editor to give myself 1 billion skill points, and then level everyone's skill levels to exactly where they were at endgame. From that I can derive exactly how many skill points were earned, and accordingly come up with an equitable distribution for the purposes of all 32 characters getting a fair shake. I'm leaning towards, for the purpose of producing the character comparison, not allocating any skill points to elemental affinities - this follows the logic of the SRW J topic, choosing to emphasize the uniqueness of each character's baseline protections. After all, I can make Cirno actually resistant to fire with enough skill points, but is that appropriate thematically? Not really.
Incidentally, I pulled the stat calculation algorithms the game uses from its Japanese wiki as well, so I could probably reverse-engineer your bonus allocations with some effort. ;) In almost all cases, I've been putting all levelup bonuses into a single stat for each character (whichever I feel complements their party role best); so far, the only exceptions have been Wriggle and Tenshi, which have gotten a 50/50 split of DEF/MND. The allocations so far (by stat):
HP/SP: nobody
ATK: Remilia, Sakuya, Chen, Cirno, Youmu, Yuugi, Aya, Komachi, Suwako, Nitori, Suika, Flandre^, Orin^
DEF: Meiling, Wriggle (50%), Tenshi (50%)
MAG: Marisa, Patchouli, Alice, Rumia, Sanae, Ran, Reisen, Eirin*, Mokou, Yuyuko, Kaguya^
MND: Reimu, Minoriko, Wriggle (50%), Iku, Tenshi (50%)
SPD: nobody
* this was probably not a good idea
^ I haven't yet recruited this character, but I'm reasonably certain this is the build I'm going with
There's certainly some room for debate as to how to allocate some characters - Eirin, for example, is more commonly given a def/mnd build, but I didn't need any more tanks so I specced her offensively (which, IMO, is so far proving to be a mistake), and some people also advocate a MND build for Patchouli. Fortunately, since I have the stat formulas, I can easily derive what anyone's stats "would have been" had I given them a different build of levelup bonuses - so for the characters which are most disputed in what is a proper build for them, I can present them with multiple builds.
At this point, there's only two characters whose builds I'm not yet clearly decided on, and they're the last two you get: Yukari and Rinnosuke.
Yukari can put out very good single-target offense if she's built for it AND if both Ran and Chen are also in the active party (note that keeping Chen in the active party during boss fights is often a very bad idea). This is compounded by the fact that if you only have one active, Chen is always the better choice for Yukari's offense, though the practical difference is small unless her target has extreme MND. Yukari is also one of the best support characters in the game with a clone of Reimu's defense buff and a spell that is essentially an AoE version of FFVI's Quick; however, no amount of leveling her DEF or MND will make her into a first string tank (but it will make her into a second string tank like Wriggle or a specialty MND tank like Iku). Another strike against offensive Yukari is that, like Eirin, her AoE attacks are garbage (but better than Eirin's at least) and so her offense is boss fight oriented, and boss fights are typically the sort of place where Yukari will be supporting more often than not. With a mind to postgame, also, the utility of Yakumo Ran + diminishes more and more as having Chen active becomes more and more of a liability (she has a hard time contributing to the postgame boss in general, as Flight of Idaten doesn't pierce huge defense well). I'm leaning towards a defensive build for Yukari, I think, but I have a while to decide yet.
Rinnosuke, on the other hand, is even more of an enigma. None of his attacks are particularly bad at all; built for attack and against typical opposition, Shining Stars of Traumerei will generate the most damage, though it's a row attack AND composite and carries all the usual pitfalls of both. The Word for World is Forest also does solid damage and is a proper AoE, and it's not composite. Start of Heavenly Demise, his most expensive attack, is actually weaker than either of those two and thus is a worthless piece of crap. His lone single-target attack is his weakest against typical opposition, but it carries fantastic defense piercing relatively speaking, so against the postgame boss it becomes his best. On the other hand, built for defense, Rinnosuke can be a passable slot 1 tank or a great slot 2 tank (though only in boss fights, given his abysmal TP). I'm leaning offensive here; defense piercing can be at a premium sometimes.