This. This is something I don’t understand at all. But, for some reason, a lot of people do this.
Ever since I first started playing VNs, I’ve always played the character routes in inverse order to how much I liked them. In short, I played the worst one first and the best one last. This is so I can 1) keep up my motivation to play the game and 2) experience a gradual improvement in the experience of playing the game as I spend longer on it, ending with the game at its very best.
The obvious inherent problem in this is that, well, the amount you like a character at the start of the game might not match at all the amount you like said character at the end of her route - some characters can greatly mature over the course of a game. For example, I didn’t think much of Miku (from A Profile) originally… including through my entire playthrough of Rizu’s route, but by the end of Miku’s route I thought she was fantastic.
The other problem is that how much you like a character does not necessarily match how much you’ll like her route. With something like Fate/stay Night, where the stories offer reduced emphasis on the heroines compared to the average VN, the disparity is going to be much larger than in a straightforward ‘pure love’ VN.
Fate/stay Night, I’d personally order the characters and routes somewhere like:
Characters:
Rin > Sakura > Saber
Routes:
Sakura > Rin > Saber
Thankfully, the latter order works fine with the order the game forces on you, meaning I got the best experience out of Fate/stay Night possible.
On the other hand, to a lesser extent, the VN Hoshizora no Memoria misordered the final two routes - the second last route is much better than the last route. They should have been swapped around. This doesn’t have much to do with the characters - both heroines are great, but the second last route is so much better, so much longer and feels ‘canon’.