I too enjoyed Bastion, but I genuinely DO see where you're coming from, Big Bob. Some of the issues you raised bothered me too, just not enough to stop me from playing through it a few times over.
It is kind've a shame that the game seems so preoccupied with constant baddie-mashing, especially considering that the few times it DOES let the gameplay take over for the story telling, it's AWESOME. One of the game's endings in particular is an EXCELLENT example of gameplay and narrative merged seamlessly. The levels themselves are never really up to much apart from masses of destructible terrain that will occasionally obstruct your path. While there is excellent enemy variety, there are some times when it can start to feel like you're just stomping hordes of identical goombas as the rush at you over a large flat plain. I guess to a degree the developers' hands were tied by the game engine.
I definitely wouldn't call it the 'most unique story ever,' but as far as I'm concerned, what it did, it did very well. Had the game come out on consoles and PC two or three generations ago, I guarantee it would have been haled as a classic for the ages and gotten its own franchise - which may yet happen, although story-wise it's not exactly open for that.
That being said, I am completely sympathetic to Big Bob's predicament. I too have in the past purchased a game off of Steam that was lavished with praises and considered and Indie Darling, but ultimately found the gameplay to be so terrible that no amount of interesting art design could save it. Also, the writing was nothing more than clunky exposition of concepts that were so obtuse I just couldn't force myself to care. That game was The Void, and looking back, I'm not wholly certain that it wasn't just an abstract dating sim dressed up in pretension and bad poems about death. I never got to the end to see if it all culminated in some grand existential conclusion, because quite frankly - after all the boring, frustrating, unrewarding and unintuitive malarkey that game put me through, I really doubt I would have even cared. Why do people like this game? I mean, for god's sake, it has a better metacritic score than Beyond Good and Evil! Not by much, mind you but ... but ... THAT JUST MAKES ME MAD. I poured FIVE HOURS into that game trying to figure out how to make it BE FUN, and I got jack-diddly in return!
So, in summation, Bastion Good, Void Bad.