Stylus is not more at fault of terrible UI than anything else. Designers simply did not design for the fingers in the first place. If they were told to design the other way, they would do it. The mere presence of the stylus did not have to change anything. I actually like using stylus and don't see anything unsexy about it.
True, it didn't _have_ to change anything, but since it was there, there was no pressure to make dedicated applications and user interfaces that worked well with touch. With a stylus, you can use normal desktop applications even though it's sub-obtimal.