Some of the winningest programs have been on the skids for a while:
Syracuse (4)
UCLA (7)
Indiana (9)
Illinois (12)
Texas (13)
Temple (14)
Marquette (15)
St Johns (16)
Syracuse is a weird case.
Syracuse in the 80's was famous for having great teams that flamed out early in the tournament.
Syracuse the past 10 years has become famous for having mediocre teams that barely scrape into the tournament, then go on a miracle run.
There has always been a certain level of instability in terms of who is good and who isn't, but I think the nationalization of recruiting plays a big role here. IU could be a national power for 20 years just by focusing on its home state, and drawing a few players from neighboring states. Illinois could be a power in the 80's just by getting a lot of Chicago players. St. John's could keep enough NYC kids home to stay relevant.
I think fewer great HS players care about staying home now, and that trend extends even to the HS level. How many top recruits move away from home to attend prep schools/academies with elite teams?
I also don't think it's a coincidence that the schools that have risen the last 10 years are mostly schools that don't even attempt to compete for the very best recruits. Gonzaga, Xavier, Butler- those are places that have effectively found alternate pipelines of talent. And Virginia and Villanova seem to target specific types that aren't really on the radar of UK, Duke, or UNC.