I liked Spirit Temple as the last dungeon because the far end of the Gerudo Desert felt like the last great frontier of Hyrule. Plus Koume and Kotake are significant enough to have a dual-form boss fight as well as their own theme song.
I sequence-broke that game as much as I could otherwise, but I never switched up Shadow / Spirit Temples beyond the 'suggested' order.
Simple questions deserve long-winded answers that no one will bother to read.