Agreed, it's always a relief to me on an Endwalker replay to be through with the last stealth sequence, like "That's done, now I can relax", and then Dawntrail brings them back. They were a little less finicky here, so that was nice, but I'd prefer just no mandatory stealth at all, as said above, keep them out of the MSQ and the quasi-mandatory aether current quests (because there's no way we'll just not care about flying).
Stealth in games not built as stealth games basically never works. And for the few times it might be fun, maybe offer an optional stealth-based side quest. Like a Metal Gear Thancred quest line specifically for fun and for stealth enthusiasts without blocking main progression because you didn't stand behind the right tree again.