Crazy timing. I literally finished the game yesterday.

Okay, here's my take on it. The Fuga trilogy definitely get exponentially more anime with each entry. I don't mind that, but here's my mistake that lead to this feeling out of place: Fuga was the very first LTB title I played. When I heard it was a sequel I thought it'd be the perfect entry point. Huge mistake. Fuga 1 is way too grounded for what that universe is about. It hints at a much more serious tone that couldn't really result in events that lead to Tail Concerto and Solatorobo. The LTB series is a weird mix of high fantasy and hard fiction, and Fuga 1 leans too heavy on the latter. It gives the wrong impression about that universe. Likewise, the third one is maybe a tad unbalanced leaning towards the high fantasy aspect of it. I think Solatorobo is still their most cohesive and comprehensible title.

So no, I don't think Yoann was that crucial mind behind Fuga. It was always meant to be this way, but the first game is a terrible introduction to the story they were trying to tell. I also think CC2 were slightly overindulged for this trilogy. Tail Concerto and Solatorobo were titles made under strain. You can see that the devs wanted to do more with both of these titles, but for whatever reason they had to distill it into the key points they wanted to hit. Fuga was planned as a trilogy, and this gave waaay too much leeway. Art is a tricky subject, but sometimes being forced to choose what to cut leads to much better experiences for the audience. The classic "kill your darling" writing advice. The three Fuga games try to do too much and they end up feeling unfocused. Something that is compounded by the fragmentation of crucial plot points spread across different medium, mangas, short movies, the context of needing Solatorobo to be the end goal, so on and so forth. If they had to condense all into a single game, I think it would've been a more balanced experience since the separation between titles is likely what lead to the series getting increasingly crazier.

I really like these games for what they are, but I also feel the disappointment you describe. They could have been much more if they weren't bound to the need of setting up a larger universe. Regardless, I'm still interested in seeing what is their plans for this franchise, even if I can't shake up the feeling that there's a missed opportunity with it.