Damn straight. Sephiroth jumped into the Mako, wtf!?! That's one of the best scenes in the game: Cloud filled with anger and wanting his rightful vengeance, pulling the Masamune out of himself and throwing Sephiroth down in his rage.
How dare Square try ruin that!
Yeah, battle mechanics can't be used. But there are other First-Class SeeDs besides Zack, Sephiroth etc. In VII you fight them in Junon, I think.
SOLDIER are bio-chemically altered super-warriors, while SeeD are augmented by the strength of their GFs. That is what makes SOLDIER SOLDIER and SeeD SeeD. So, in this argument, one cannot consider SeeDs who haven't junctioned or SOLDIERs without Mako.
I personally feel (as stated above) that SeeD would edge it, marginally. I think that the Mako should nullify the effects of Junctioning, so it would basically come down to skill. And SeeD are trained at a younger age, and are constantly fighting in tactical warfare. SOLDIERs are older when they join, and are more special-ops than involved in tactical warfare. Thus, SeeD have the minor advantage.