First method is order of magnitude more complex, but it is better
Until nanomachines, which maybe an order of magnitude harder than even first method, u can't avoid scar tissues, and it won't be good especially when it all over the body parts.
So considering the amount of work and internal connections required, of allsorts of tissues and vessels, second method may be on pair with complexity of a first one (if by brain transplant we loosley mean head transplant as well)
Difficulties of second method are in finding apropriate parts, which won't be easy, they do have to not reject themselfs. But as a solution is potencial stemcells 3d printing of new organs, or other ways artificially to grow them. I seems have seen some results on both of those(3d printing, and growing - small pieces very limited) but if we talk about random parts and organs, all of them, it seems to be even harder than head transplant.
So on a scale which you would like it to see, replacing all, I would say that head transplant is closer to reality as for today.
Topic is quite old, even its recent development, some sucesses are reported(on animals), but not sure about results with this guy https://en.m.wikipedia.org/wiki/Sergio_Canavero he prepares for that for a decade already
So if your villan needs a transplant near 2023 go with a head one.
If it is nanomachines son time, then go with brain transplant and freshly cloned/printed body as one of the options, never trust those digital uploaders, go with good old stuff.