There are plenty of ships for very minor characters that I simply haven’t developed yet for this AU that I am neutral on. I have a lot of ships and fankids for this AU because I wanted to create a fully fleshed out ‘next generation’, but that means that there are many adult ships and fankids who I know nothing about. So, in that sense, those ships that I have not thought about much yet would probably be the ones I ‘like least’, just because I don’t really have much of an opinion on them yet aside from that it is canon in L&L.
As for ships that used to be endgame and changed, there are a few, but the reasons behind the changes varies. In most cases, I simply found a ship I liked better, rather than growing to like a ship less, if that makes sense. For example, originally, Brendan was married to an OC former Team Aqua Grunt named Louise and Eve was their daughter, while Wally and Anabel had Layla, Rhys, and Edward. However, over time I grew to really like LoveRivalShipping, but also was still fond of MirrorWorldShipping, so I decided that Brendan/Wally/Anabel would be an OT3 so I could still have both ships be canon. I cut Louise from the story and merged Eve with the rest of the children, then changed the parents a bit and it all worked out. A similar instance occurred when I realized I really liked HonorShipping, but Falkner was already married, even if Morty was single. So…. I killed off Janine (not my greatest moment, sorry Janine). In that case, I guess you could say I grew to like FatherlyShipping less, but it was still mostly a situation of me growing to like HonorShipping more.
Another instance is mainly just caused by the restraints of the AU. My actual favorite Ash ship is PearlShipping, but there are many reasons that ship wouldn’t work in the L&L universe. The Dawn in this AU is very different from her anime counterpart and so the dynamic between her and Ash would be very different. I also have endgamed Dawn and Jeshir for a long time, and I wasn’t going to change that ship just since I had decided that Ash existed in L&L. As such, Ash ended up in what is probably my second or third preferred ship for him, ComaShipping, since that’s what fit best in the universe. The same could be said for many anime pairings though. In the anime, I like ContestShipping, BoutiqueShipping, and JellowShipping, for example, but since the world of L&L isn’t the anime, those ships didn’t make sense for one reason or another. It’s not that I like the canon L&L ships any more or less than those ones, it’s just that in the context of the mainly game-versed base AU, I prioritized my preferred game-verse ships, like ContestQueenShipping, KalosShipping, and SnowLilyShipping.