I never played the 2008 PoP reboot, but the Sands of Time trilogy I played to death.
I'd say Two Thrones is the best overall. Sands of Time has too simplistic combat, Warrior Within has great combat but also those annoying Dahaka chases and terrible boss fights. Not to mention the music, art direction and atmosphere wasn't very PoP-like.
Two Thrones kinda combines the best of the first two games, but has the negative of throwing in the "Awesome Button", i.e. speed-kills.