I've done 4 Six Flags
New England
Great Adventure
Magic Mountain
Discovery Kingdom
Coasterwise, I'd say GADV and MM are pretty much neck and neck. Whilst GADV had Ka and El Toro in its top 10 worthy rides, MM had X2, Tatsu and Riddlers. On the clone side Medusa are better than Scream but Magic Mountain had the way better Batman: The Ride . So I'd call that pretty even.
Discovery Kingdom was easily the most well run and clean park out of the 4 with the best operations and some good rides such as Medusa, Roar and V2.
New England had Superman though which still remains my #1, even if they have transformed it though.
I'd call all 4 pretty even if you take everything into account, but if I had the opportunity to revisit one right now it would be SFMM, because outside the coasters, Great Adventure was a bit of a dump.
On the question of the best of the more unsung parks, I'd probs go SFDK, as it was a really nice and pleasant park with good operations as well as some damn good coasters. If I had been to SFFT I'd imagine that would be top though.