I would say the main reason to pick the 5spd manual Prelude is the 4spd auto transmission in 6thgen Accords are notorious for failing, both for V6 and 4cyl. It is not guaranteed it will fail, but it is a possibility. A lot of V6 owners have swapped to 6spd manual, I did even though my auto was fine when I took it out at 133k miles. Plus a manual is just plain more fun to drive. I knew about the V6 transmission before I bought my car back in 2007, but I just didn't want to drive a 4 banger so I took my chances.
I don't know much about the Prelude so I can't speak to its reliability, but it is a 4cyl manual Honda so I think it's hard to go wrong. I've just heard to stay away from the SH model. As for looks between it and the Accord, it's a matter of personal preference. Both are good looking cars imo.
The 6GA also doesn't have much of an aftermarket, I would think the Prelude does but I don't know for sure. But the nice thing about the Accord is it shared a lot with some Acura models of similar years, so there are some nice OEM upgrades available. And it might be easier to find parts for it as well since it's more common. But if you want to make power with a 6GA, it takes a lot. Maybe that's the same for the Prelude, again I don't know.
Anyway there's a few things to think about or look into, hope it helps.