Okay, HRtP and SoEW's cover art clearly depicts Reimu with black hair with purple highlights.
That is very much a point of contention. To me, Reimu's hair looks much more purple than black, though it should be pointed out that HRtP's and SoEW's cover arts have much stronger colors than the other three games.
(Notice that Marisa uses the same color as Reimu.)
Marisa in LLS (in-game, I mean) has a very vibrant purple as her dominating color. It didn't actually get darker until MS. Granted, it's still darker than on the cover art, but maybe ZUN just didn't have that particular shade on hand.
As for Mystic Square's results screen, it could very well be a palette issue. The results screen doesn't use as many colors as the title screen, so he was free to be more liberal with Reimu's color scheme. Plus, she looks very-much like how she does in the Windows era. It's probably coincidence, but I'd like to believe otherwise.
Yeah, no, that shit ain't gonna fly. You make it sound like ZUN designed the title screen background first and then put Reimu in like she was an afterthought. Also, the notion that palette constraints forced him to draw Reimu with purple hair in every single instance
except for Mystic Square's results screen... Jesus Christ, are you even listening to yourself? ZUN is a smart person. He would have been able to depict Reimu with black or brown hair if he had wanted.
That really doesn't say anything about the PC98 games, does it? The Windows platforms have a much-higher color depth than the PC98 did, so it made much more sense to depict a small character sprite with a more-vibrant color. Konngara, on the other hand, is a much larger sprite, so he can afford to add details like highlights in his/her hair. Plus, Konngara's hair is up against a blue background, so black actually stands out in this case.
You say that like sprites are the only thing that matter, entirely disregarding dialogue portraits. Besides, 4096 colors is nothing to sneeze at, especially when it gives you 16 shades of gray, black and white included. I'd say that would have been more than enough to depict a black-haired character, and ZUN could have made everything else fit around that no problem, I'm sure.
Looking at Reimu's sprite, the colors that pop up the most are red, green and black. You've got a couple pixels of purple there, but it's really insignificant when compared to the red of her ribbon and skirt, which draws the most attention and directs you to the rough whereabouts of her hitbox.
