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I would start over just because it's been ages since you've played the game. If you start over you'll probably do a lot better than when you played it through for the first time :) But, if you don't start over your able to go back and get all the things at some point.
You could just get Yojimbo to do Zanmato against the dark aeons
... there's no reason to restart.. until you (SPOILER)beat Seymour for the first time, you can walk all the way back to Besaid to get whatever you missed there. Dark Valefor won't be there yet, so you won't have any problems other than a slightly long walk.
I could backtrack to Besaid, sure. There's one little tiny thing.
Cloister of Trails is closed until the Highbridge. =P
Which means that I'm NOT backtracking to Besaid for the damn Al Bhed II. @_@
And... uh, I can power up my Aeons and use Trio of 9999 on this fight, right? Tidus, Wakka, Lulu and Rikku have multitarget attacks/Overdrives anyway, and Rikku has Hyper Mighty G for Auto-Life =P