I really don't think the references were that much more timeless before the "break". There are plenty reference-points that really stick out as early 2000s like that episode based around Napster, and a videogame bit that referenced Nintendo 64 and All Your Base Are Belong To Us.
Quite enjoyed the new da Vinci one - some nice throwaway jokes, albeit not at the rate of the classic episodes, and it wouldn't have looked out of place in the original run. I think they're in danger of making Fry too dumb in a tedious way though, a bit like the way Homer Simpson went.
It was just for the sake of this story though I think, he hasn't been noticably more stupid in previous weeks and I doubt he will be in most future episodes, but there was an actual reason why they seemed to be making him more stupid than usual, even though it is slightly lazy to do that I can forgive it since there were some funny lines. Also it was a new/freelance writer who wrote the episode so that might have something to do with it.
Absolutely hated the montage at the end that was trying to be like Luck of the Fryrish/Jurassic Bark but just felt so contrived and stupid.
"I'll just have to shoot Hitler from out of the window. Oh no! I've hit Eleanor Roosevelt!"Even though I more or less saw it coming, Prof Farnsworth slipping on the lever a second time had me howling.