An I6 would mean more room in terms of engine bay width and cheaper mods since you wouldn't need twin parts(2manifolds,pipin etc. . .)
But the vq series imo is the most refined and smootest(strength and refinement are 2 different things, i.e. rb's are thier strongest ofcourse)series of engines nissan has ever produced imo even if it isn't an I6. Just driving a 350z told me that. What a marvelous powerplant.
A heavy one at that though, it's the reason why the z doesn't feel happy in low speed handling and complex cornering and it's the reason why thier isn't anything around it other than learning how to deal with it(i've always told people this, when you drive one and if your the type of driver that can sense things right away you get the feeling that it would take more than weight reduction and suspension to fix it) read the latest scc where they took a z and stripped it from front to rear, replaced the windshield and liftgate(yes the liftgate and window that it holds) with lighweight plexi,suspension,bars and did some other stuff. They removed a hell of alot of weight.
You can still have a balanced car with a v engine though ofcourse but I doubt it will be.
There are cons to having an I6 and pro's to having a v engine.
I6's are long engines and v6's are usually half of an I6's length, a v6 is usually shorter than most I4's also. You can have a shorter front end,shorter hoodline,shorter car overall with a v6 as opposed to an I6 where you'd have to design a car's lines to accomadate the long block. Now before someone mentions rb's into 240sx's, Rwd cars that have I4's usually swap well with I6's because you only adding 2 more cylinders anyways and cars with rwd I4 layouts tend to have the classic longhood frontend design(240sx,miata,s2000etc. .) so thier's always extra room. If you can make the front end shorter than you can increase overall interior room especially in a coupe configuration where you could adopt a cab forward design.
The negative thing I see about a v6 is space to work in terms of width under the enginebay and the priciness of mods and quite possibly a noseheavy car.
If you can afford the new gtr, you could probably afford the mods anyways.
I'm predicting that pricing will be double of what the z is.