Wow, that's a much longer answer than I expected, thank you! Going to try and explain myself a bit better.
I did get the best ending on my second or third replay, that wasn't a problem. The problem was more that I ended up doing mostly redundant events that locked me out of the ending. For example, I went to the docks twice (getting the bar and the Red events), same for the Lighthouse (getting both of weatherdude events) but, as I realized on my next games, there's no real point to doing either, since the Red intervention at the end of the game gets overridden by weather guy, and the second lighthouse event doesn't seem to have a huge impact.
The evolution wasn't really a problem on my subsequent runs (even figured out the Houndoom capture), since I understood you needed two fights (or one+Janine training), but I just wanted to point out it's perfectly possible to get through the entire game with like, one fight and get most of the clues. I think it'd be good to have a comment about Beldum evolving soon, because it's easy to run into one fight, barely win by having Beldum spam one move (especially at the lighthouse), and think "okay, I'm useless in battle, better focus on investigation stuff". The fighting in itself was good (this is a VN after all), I just feel there was a bit of a disconnect between it and the narrative.
I didn't know you needed four clues, but I suppose this is linked to the TM stuff? I think there should be a bit of a change here as well. If I'm getting this right, my first run had me get the two clues at the Pokecenter, the one in the lighthouse, the one at the bar, plus the Gyarados thing during the last day. I didn't get the TMs, however. The only change I had in my next run was learning about Mightyena after the Houndoom fight, which triggered the TM scene. The problem here is that this last clue shouldn't really be the trigger to obtain thunder punch, I feel. I mean, it's what makes you win against Mightyena, but if you just know you're going against Team Aqua, you'll know they have water pokemons, so that should be enough to get thunder punch.
I dunno, I just feel like there should be a better explanation as to why you don't get the TMs, or a change in the number of clues. It doesn't make a lot of sense to know they have 6 Gyarados(es) and a few more water mons, yet still be locked out of thunder punch.
I honestly think this is really good for a first game, don't worry about that! It's just that, as a player, it felt a bit weird to have the MC be unable to come to the same conclusions as I did, and have Cynthia do the work instead. Although, I guess this can be handwaved by him having a defined past already.
Anyway, again, thanks for answering! This is actually one of the first Pokemon fangames I've ever played; most of them often bore me before I even reach the halfway mark, but this one kept me hooked for a bit. So, good luck to you, and keep up the good work! Can't wait to see what the next update looks like!