If you are talking about MGSO 3.0, I use it too. I picked all the vanilla options during setup and think it looks very much like the vanilla game I remember from playing on the Xbox, but in high resolution.
If you haven't already, you may want to update your MCP and MGE XE and unofficial patch since the MGSO versions are outdated, and do the bug fixes listed in the opening post of the MGSO thread. But I too play with a MGSO installation, with a few select mods added on top, and I enjoy it very much.
As Tujira said, make sure you installed all the fixes and updated the mods from the http://www.gamesas.com/topic/1513057-relz-morrowind-overhaul-sounds-graphics-30-thread-6/?p=23874308.
By DLCs if you meant the official plugins like bitter coast sounds, Le Femm armor etc, then make sure you get the cleaned and fixed versions http://download.fliggerty.com/download--1079.