Hey now, to be fair, there is the occasional story that actually explores the CB and what it means for both Earth and Equestria. Every once in a while, there is a CB story that is actually rather interesting, and not too bad of a read.
That said, yeah, it usually boils down to wish fulfillment. Though, I feel the need to mention the other side of the coin: the Anti-Conversion Bureau, the side that hates the CB and what it's usual fans think of humanity. These stories typically show the ponies as nothing short of monsters, lead by Tyrant!Celestia in a war against all of humanity. The humans then roll in, kick some flank, and then roll out, proving that the Equestrian's fears were absolutely right. How ironic. Thee stories are usually just as bad, just praising humans instead of ponies. Ugh.
Wait, what? The original was not that bad? Dude, that fic sucked. I mean, nothing against the author, he's actually a pretty cool guy who can write well enough now, but the original Conversion Bureau was awful. I mean, not like Cupcakes level awful, but still pretty bad.
Actually, if you were not planning on taking the original, I was thinking I may do something with it. I mean, I have My Little Unicorn ahead of me already, so it's not like I need another infamous badfic, but I've been thinking of some things I could do with it. But, if you were planning on taking it on, by all means, have at it.