If you want to be able to switch between those installs - check out http://www.gamesas.com/index.php?/topic/1142151-rel-mtes4-manager/. I have two full installs with a lot of mods each and Nehrim and a vanilla/tinkering install. That too helped - I can think "Oh this mod might fit better over here than there."
You do bring up another major difference - Oblivion modded can still stress even the most recent hardware. It is so easy to mod Oblivion to cripple my computer. I don't think it is that possible with Morrowind unless you set everything in MGE to max.
So yeah Oblivion can be about balancing stability with new content. It is often one or the other - less content more stable - more content less stable.