The biggest problem with skill trees is that everyone will just fall into the default, cookie-cutter build because some theorycrafter somewhere proved that it is 0.0002% more powerful, and people will be chastised for having the "wrong" build, and will be forced to justify their decisions.

Don't get me wrong; I loved the freedom that skill and talent trees brought to WoW before MoP nuked them from orbit. I loved making a PvProt warrior who borrowed self-healing abilities from Arms and Fury, and who focused around interrupting the enemy team to make them try to kill me (when I'd built myself to be very hard to kill), distracting them from the objective. But I did not like having to justify why my build deviated from the "best" one whenever I got into a PUG.

The other problem with what you're suggesting is that it would wind up going the GW2 route: players would take hybrid builds and use the overpowered nature of them to cheese content. Instead of a party of two tanks, two healers, and four DPS, we'd get eight tanking, healing DPS players who just zerged the content. The trinity would evaporate, because there would be no way to prevent hybridization, and no way to balance content for it.

Given the headache that balancing classes can already be, I'd rather SE focus on maintaining the balance they've already established, and not try to account for different builds.