I replaced my Ultegra Hollowtech with a White Industries square taper bottom bracket and crankset. I was very concerned about degrading the performance, but so far (almost a year) and it seems just as good. (I wanted to get the White Industries crank with the 30mm Hollowtech-equivalent, but unfortunately it wouldn't fit in my BB shell with all my Di2 junk.)

All other things considered equal, I would choose the Hollowtech option, but a well-made square taper will be perfectly fine too.