Have you tried starting as new game or gone back to a low level save? I had the same symptoms back in June, just prior to the 1.5.80 update, caused by some crap or another I'd installed along the way (for instance, I was running both MFG Fix and Opparco at the same time, I had installed (and uninstalled) a couple of LE mods accidentally, etc etc). It (whatever "it" or "they" were) eventually broke my saves from the (at the time) current level 52 character all the way back to when she was only level 16. That is, everything from mid level 16 up through my at the time top level was borked. Very slow gameload times, slow cell transition times (also very slow..several minutes) somewhat routine CTDs, etc. That is, when they'd even load in the first place.
Another one I ran into later is "too many animations". When you have too many animations loaded (and don't go by the published max, it can hit far earlier) the game can bog down really bad. Your MCMs can stop working. animation drivers like SL can fail. Papayrus can get choked up by too many scripts running. etc. etc.
And not to hijack the thread, but if anyone knows how to clean saves of papyrus stuff (beyond the simple resaver technique) I'd love to strike up a conversation on that. Methinks many of us could benefit by getting a handle on that issue, since suspect a ton of the complaints about CTDs and sluggish performance could be addressed if we could get a handle on it...but I digress.
Try opening some really low level saves and see if the game works normally. Your issue *sounds to me like mine, and mine was accumulated crap in the save as I leveled her up. Partly my own fault, partly just normal build up of junk.
Oh, and if you happen to be like me and carry around an unnatural amount of loot (afaik my female character is carrying around 7800lbs right now, and the male character has around 22K lbs in his personal inventory), purge it. purge it hard. If you don't have one yet, find yourself a player home and dump that junk into chests to get it off your person. FWIW, on that subject, Peregrine Highwatch is one of the best player homes I've seen so far, and it has a ton of solid storage space (solid: ie, it is trustable, unlike some of the other player homes like underground bathhouse) . Worth every Septim I "paid" for it.