The reason (I think) for more .357/.38 New Vaqueros (and even the original Vaqueros) is three fold. 1) Ammo availability for non-reloaders, and 2) In CAS, there is the need for powder-puff loads for speed (pop pop pop pop ... pop). 3) cheaper to shoot. Also for some ladies, it is easier to handle.
I know which I would pick .... .45 Colt .... for a myriad of reasons.... But really it all depends on you and your needs/wants. For example, you plan on target shooting a lot, but don't reload, and don't have deep pockets, then the .357/.38 route is the way to go. If you are after traditional SA Old West type shooting, the .45 Colt is the way to go.... Think how you intend to use it.