In general, whereas the OT comes across to me as a timeless, lighthearted and epic fairly tale, the PT just comes across as a commercial turn-of-the-century marketing effort. As far as Episode 1 goes, I don't feel anything for any of the characters, except for Jar Jar who still fills me with contempt every time he shows up onscreen. Even most of the other aliens either act or look corny and cartoonish: The nemodians, Boss Nass, Watto, Sebulba, the pod race announcer creature and even the charismatic Jabba we knew from ROTJ has been turned into a visage for slapstick comedy in this film. Episode 2 and 3 did only slightly better. The OT introduced C3PO, R2D2, Jabba the Hutt, admiral Ackbar etc. There's just no comparison for me.
As for the perpetrators of the PT, Darth Maul has always appeared to me as just another very uninteresting, old and kitchy style satanic character that wasn't given nearly enough screen time to be an effective enemy. This is much of the reason why the final saber fight in Episode 1 has no emotional impact on me whasoever. Dooku in Episode 2 is better executed for sure, but I still don't care. Give me the OT any day of the week.
When it comes to costume design, the PT has nothing that comes close to the visual coolness of stormtroopers, TIE pilots, snowtroopers, biker scouts, Darth Vader and Boba Fett, except for the obvious variations on the stuff created 25 years earlier. I don't really care that the imperial soldiers can barely see through their helmets, the OT wins hands down. As for spaceship and set design, I'll take the death stars, TIE fighters, X wings, Y wings, Millennium Falcon, star destroyers, cloud city, AT-ATs and AT-STs over anything I've seen since.
Save for a few pieces of music, I also find John Williams score for the PT to be rather uninspiring. I don't think he is as creative today as he was in his earlier years, but what he was given to work with for these films didn't make things easier for him of course. The fantastic score of the OT is an integral part of the films that contributes immensly toward keeping the viewers emotionally attached and some of the pieces stand well even on its own, without the movie to support them. As far as sound effects go, the OT gave us the on/off, hum and clash of the lightsabers, the blazing lasers, the shrieking TIE-fighters, Vader's breathing and voice and the list goes on.
I'm going to download ADigitalMan's edits of Episode 2 and 3 as well, since this is probably the only way I can make myself bother to watch these films again, and I'm sure I'll enjoy them much more than the theatrical and DVD releases.