They're still there! They've just been in hiding for a while.
Accidental Edutainment isn't easy to do well. Disney succeeded for the 80s audience, but by the 1990s, Epcot seemed heavy-handed. We all agree that Epcot lost its focus in the mid–late 90s—in fact, one could argue that the entire company lost its focus as Eisner concentrated on bloating the Company to a ridiculously large size. Maybe he was overcompensating for something.
Anyway, IMO Epcot lost its optimism for a while, but that spirit of inspiration is finding its way back. Look at the post-show games after SSE. Look at the exhibits following the Nemo ride (Turtle Talk is now disappointingly pointless). The countries have been slowly but surely getting their identities back from Disney merch—Norway isn't even overrun with Princess crap any more. The Land still teaches and inspires, and UoE still bores us to death with unfunny Ellen Degeneres.
New exhibits in Innoventions are gradually returning to Communicore tech and away from outdated video game cheesiness. M:S is pretty much the only straight, meaningless thrill ride.
The core values of EPCOT still exist, and upcoming updates should continue to bring back the spirit of discovery that disappeared with the advent of tarps, whirligigs, and tombstones.