I went through a big debate with myself (most of it was non verbal lol) about if i could deal with an auto when i bought my car. I just couldn't do it. Stock for stock, i really didn't feel the v6 felt much quicker and to me, percieved power is what makes you car fun to drive. I will say that the v6 is WAY smoother than the 4banger. But the tranny sucked even for an auto. So i went with a 4 banger MT.
At the time, i had no clue how problematic the v6 at was. I think i made a very good decision. And for the price, a 6 speed swap is a bit much (especially since i really don't see why it didn't come with the v6 in the first place). I would have no doubt bought a v6 5/6spd if their was an option. For the price of a swap, it's hard to say if i would do an h22 and have some money left over for more mods or a 6sp v6.
I do think the v6 is the way to go if you want to spend alot of money and make the "ultimate" accord. After seeing vids of mikeys car, i was jealous to say the least. Pair that with a supercharger, and possibly a tl motor, you have a realtively stockish car that is really respectable. I'd personally go with another car.
Sorry for the essay, i'm feeling last night a bit, lol. Thinking and writing makes me feel better.