Engine swaps, I'd go for that, as long as the engine isn't stupidly large for the car it is in.
Drivetrain swaps, I don't like the idea of messing with cars. I would say depending on where the engine is in relation to the existing drivetrain, I think it would be ok.
Example, a Front engined, front wheel drive car in order to become 4 wheel drive or Rear wheel drive, needs a driveshaft to go down the centre of the car (Well, from my very basic knowledge of cars, it does). If there isn't room for it, don't allow it.
Cars which are already 4 wheel drive should be changeable in any way. Some cars, like a Porsche 911 Turbo, should be able to be modified for Rear wheel drive. But because the engine is at the back, presumably that means it will be lighter because it doesn't need to send any of the power to the front by way of a driveshaft? And providing the weight and handling characteristics are accurately represented, so we don't get ridiculous balance issues like Forza 3, I think it is an excellent idea.
Could we even go as far as saying, cars with 4 seats which are Front engined, rear wheel drive, should be able to be modified so that they are midengined? Or is that going to far, or is it not possible?
However, it is a bit late to be talking about 'should X feature be in Gt5' because they don't have time to start developing anything new.