I enjoyed BT way more, with the notable exception of the final boss. BK has to this day what I consider the best final boss in a 3D platformer, that I've encountered at least. (Except for the fact you can't repeat it without copying your save first. Hopefully the XBLA version fixed that.)
I could imagine hating the FPS segments in particular if I played it again, though. I wasn't crazy about those in the first place.
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"One toot on this whistle will take you to a far away land."
-Toad, SMB3