Since Sora isn't evil at all he became the weakest heartless.
Isn't the weakest/most friendly heartless the White mushroom. If anything, that is a good heartless so he should have become that, but I see your point. The mythology is pretty complicated.

how did beast get to hollow bastion?
I thought he said that him and his world was being consumed by darkness. As he longed to see Belle with all his heart and with there connection, he appeared at her location.

why isn't rikku the hero when he is linked directly to terra in bbs, but sora isn't but barely linked to ventus?
I think Riku metioned this, something about how he chose the darkness in order to leave Destiny Island stopped him from being a keyblade master at that time. Sora happened to be was next in line.

why is neverland in EVERY kingdom hearts game except 2?
Captain Hooke was already dead and consumed by darkenss by KH2 because he was defeated in KH1. BBS was before all that so he is still alive and can be used in a story.

why is agrabah changed so much in 1 and 2, same with halloween town?
Fund raising and renervations thanks to Jack

how does merlin live in radient garden but without it being completely destroyed he is in traverse town?
Similar to how Sora appears in traverse town. Radient garden was his real home.

Why is Sora voiced by a girl?
I thought he was voiced by Halley Joe Osmant....is that not a boy? The "I see dead people" boy?

How is it that terra goes to cinderellas castle after ventus, but is at the dwarf woods before ventus, when that is the first place Ventus goes????????????????
Very poor storyboard planning by the writers. That confused the crap out of me. A similar thing happens later on as well.

the answer to all of these is: I T I S A G A M E
Its not a game, its a way of life........not really. It is just a game, but I have a bad habit for analysing things a bit too much. I'm just not happy until I understand it all.