Sorry if the title was undescriptive. What I mean is after progressing with a certain character over time the game seems to run slower, Like with my followers I have AFT and when I level up they use to level up instantly after setting my perks, now they level after about 3 or 4 min. Another thing is my game seems to take longer to start up with SKSE then what it use to same with the title menu the options to continue ect. have a delay on showing up. Also load screens have gotten longer, This wasn't an issue on my clean install/ new game and i had more mods then I currently have. Is there a trick to keeping the game running as fast as a clean install? Again sorry if I'm not making much sense.

Well, a trick? No.
But it can be done.
You have to be willing to make the effort to do so.

http://www.gamesas.com/topic/1452049-area-transition-to-blank-screen-or-endless-loading-screen/page__view__findpost__p__22441688