TPM>ROTS>AOTC.
Phantom Menace has Jar-Jar, but it's got the best set pieces, the best Jedi not played by Ewan, and the best Sith of the prequels. Plus Anakin was annoying but not ungodly dumb like he was in AOTC and ROTS. It also was the least flashy of the bunch, which I felt worked in its favor.
AOTC is a clusterfuck that I'll never understand. Anakin is awful, Padme is awful, the whole Jango/Boba idea is awful, and the set pieces got too nuts (looking at the arena and factory sequences). Plus the ending was weak and Yoda had a lightsaber. No thank you.
ROTS is a mixed bag, and while it was my favorite for a while it grows weaker each time I watch it. All the Jedi are killed in a dumb way, Anakin's fall is completely unbelievable, Padme's death qualifies as one of the worst deaths in cinema history, and there was no single villain that stood out (at least for good reasons). I feel like the spectacle was there at release (Mustafar duel looked amazing at release), but it has aged horribly. ROTS' opening had such promise, with a great space battle, a cool rescue, and the second best duel in the prequels, and it did nothing but falter after that.
So, basically, the prequels suck as Star Wars movies and are at best mediocre sci-fi films.