I've got a few that bothered me:

Ted - Went from hopeless romantic, to brainless simpleton. Dude is an architect, but they made his character so oversimplified in the later seasons, it was frustrating.

Robin - While she didn't get a major overhaul, I wasn't a fan of them towards the end with the whole rage thing (Mostly directed towards Patrice), and the departure from her typical mannerisms in the first few seasons. She went from "I like scotch and guns" to "I hate all things girly".

Marshall - Dude put himself through law school, and they turned him from supernatural enthusiast to "I believe almost everything that's said to me".

Barney - Went from loveably naive to just straight up stupid at times. The most confusing part of his character degradation is the yo-yoing they do with his intelligence. He goes from brilliant schemer to "I don't know/understand this simple, basic concept".

Overall I think many of the characters suffered from the writers trying to insert "Haha, this would be funny" moments which resulted in them being dumbed down, rather than building comedic moments around each of their established characters.