I don't have feedback on every boss; most of them are fun and about the right level of challenge.
Stealth Snake: Appropriately easy for the first boss, and a good test of what you've learned. The first dungeon is all about knowing which enemies to use Dark Attack on, and which to use Silence Attack on; for the boss, you just need to use both.
Phantom 1: This felt like a rehash of Stealth Snake, with no new features.
Craig and Brianna 1: Great boss, a nice step up in difficulty but not too much of one.
Meganom: Unlike Nepster, I took out the Nom Plants first. This was also a good boss fight.
Spirit: Mostly fine, but "Drain"-spamming got really annoying.
Transient: I like the puzzle of analysing the attack pattern, and defending before Trauma. However, even having solved this, the boss is likely to be too difficult for the levels you have when you reach it, forcing the player to grind. I'm not sure the best way to deal with this (and I'm going to have a go at starting a new game and attempting it at low levels, to get more of a feel for it), but even having five Softening Sand instead of four would make a difference.
Craig and Brianna 2: Awesome fight, one of my favourites in the game.
Grand Obbie: Seems impossible to survive Disaster at the levels you're likely to have before re-entering the Metaspe, when this fight becomes unavailable for a long time. When it's next available (after Dark Transient) you're about the right level for Disaster, but the entire rest of the fight (and the dungeon) is extremely easy. So, Disaster seems to be the part that needs changing. I rather like Nepster's suggestion of replacing it with Deathly Rain.
Microsient dungeon: This is where I gave up the first time I played the game. This time, I had enough AP to give Leanna Breaker Attack. Split Attack is also excellent for this dungeon. But it seems likely to be a huge roadblock if the player has made bad choices for which abilities to get. Again, giving more Softening Sand would be a lifesaver.
Craig and Brianna 3: Very hard until I got the idea to use Zombie, which was a lovely "aha" moment. But the fight was disappointingly easy after that. As I said above, I'd prefer it if draining Brianna's MP was a viable strategy, both so there's another way around the roadblock if the player doesn't click onto the intended solution, and because the fight would still be difficult.
Dark Returner: A very nice challenge. This boss really depended on understanding the mechanics and working out a strategy.
Dark Transient: Awesome. Probably my favourite boss of the game so far. This one
really tested your understanding and strategy, and since every action counted, it was nail-biting all the way to the end.
Test of Knowledge: Okay idea, but the repeated questions were annoying. "Use something helpful" should totally have accepted Regen. I'm sure you could think up some harder questions for this.
Bolder: Pretty hilarious, since buying Omni Resist for everyone completely neutralised it. The finale, where Explode takes out a random party member and deprives them of AP, was really annoying.
Aisha: Long and tedious, and then she makes it worse near the end by casting Wall.
Yuki and Sasha: You've already addressed my complaint here, which was that it should be easier to get Sensor Spheres. With that out of the way, it's a pretty good puzzle boss.
First Weapon: Awesome! In spite of the very high HP, this was a really tense and enjoyable fight -- partly because so much was riding on it, whether I'd be able to get out of the cave and enjoy my loot, or have to go back to an earlier save.
Warrior Fish / Golem: Simple. Both can only single-target, so they can be taken out with physical attacks and reviving any knocked-out party members. Golem's very high defence makes this laborious, so I looked around and spotted the Zombie+Regen weakness.
Phantom 4: Excellent boss. But much harder than Warrior Fish and Golem, so why does it give less AP?
Craig and Brianna 4: A tough challenge. You've already addressed my main complaint (the unfairness of Craig's instant death attack) so all that remains is the question of whether, after the changes, the fight is reasonable for a party that hasn't done the cave dungeon. And I can't really answer that one
Wraith: Interesting unusual mechanics. I like the way that, counterintuitively, remaining at
low HP is useful, and that this is achievable with Phoenix Dust, pretty cheap to obtain. Nepster points out that it's vulnerable to Regen, so perhaps that should be removed?