Bugger..
I'll have to cut a serious amount of mods as 3 minutes just feels broken.
Some info regarding this case:
Skyrim Revisited install + a few extras (SkyTweak and some other small mods)
File operations for TESV.exe from pressing "Run" in MO -> main menu to appear: 4 638 368 and it takes 3m7s.
For a clean install (through MO): 238 854 and 21s.
Both with SKSE on.
1m 15s to juggle around with ini files only seems odd to me. Mostly the initweaks.ini (create, query, close, lock, read, unlock, close) and then atleast thousand times (if that's enough) "create" for every esp/esm. For every esm/esm ini CreateFile operation the result is same, "NAME NOT FOUND".