Let's see ... how did TNG fuck things up ...
In no particular order:
All the pseudoscientific technobabble. I don't remember TOS ever resorting to this crap to any significant degree.
The stupid "The Federation is a 110% perfect, atheist utopia that never does anything wrong and never uses money" crap.
Making it so that there is never any major conflict between the main characters of the show. Everyone just always gets along like one big, boring family from some '50s-'80s sitcom.
The overuse of human and rubber forehead aliens.
Turning the Klingons into stupid, dirty, one-note brutes.
Never allowing the interesting characters like Data to ever significantly grow and develop.
Oh, and IMO, DS9 didn't fuck up Star Trek. If anything, it rectified some of the damage that TNG had done and restored some of the fun to the ST Universe that had been lacking in it since the TOS films had come to an end.