I agree that they built the Reapers up too much to have a reasonable solution to them. But I don't think it bothers me all that much that the unreasonable solution was "blow them up with a really big bomb". That it was such an oddly specific bomb... yeah, that bothers me.
Otherwise it's just like... Lavos. So powerful it can manipulate the flow of time and space, brainwash people to do its bidding, alter and guide the genetic evolution of an entire planet's lifeforms... but Crono whacking it in the face with a sword a dozen or two times is enough to put it down for good (until the sequel).
EDIT: Also, I think I'd hate the the Crucible a hell of a lot more if I'd played the game before the endings got expanded on. Back when it was just "pick the color of your ending".
Also also, I can't believe this slipped my mind, but the very idea that you can only use the weapon made to destroy the Reapers with their explicit approval just baffles me. But that's just another reason for me to say "Removing the Starchild would make the ending better".
Where Dynamis gets me is that it's not even remotely clear that it was necessary to enable the final confrontation with Meteion. All it's ever used for is emulating things that other power sources could already do. Limit Breaks were explicitly aether-based until the Endsinger opened her mouth to squawk "dYnAmIs?!" at us. The telepathy and universal translation stuff was stuff the Echo could reasonably do... or already did. As was the whole "transcending your limits" thing. It's literally called Transcendent Power or something rather than "the Echo" in the Japanese text, iirc.
It's like Dynamis is trying to be the Unreasonable Solution to the Insurmountable Problem, like the Crucible/Catalyst was to the Reapers. Except the problem doesn't seem nearly as insurmountable as the writers wanted it to be, and more reasonable and less genocidal means of dealing with Meteion seem plenty viable as well.