The .38 Super is a terrific caliber, but unless you're into reloading your own ammo, I say you should go with the .45acp (hands down)...
That said (from an "investment perspective") a .45acp will tend to be "worth more". Now I'm not going to try expounding on all the aspects of firearms ownership vs. investment - but I
do feel that considering the re-sale value in any piece is a subject well worth consideration.
On the other hand, if you have a deep desire to own a .38 super, this could be the pivotal event that brings you to consider becoming a reloader (if you're not already).
So while my comments are somewhat convoluted, I'd defend them simply by saying the best bet is to own
both calibers
and take up reloading (if you haven't already)