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What's your perfect game? For me: It'd have to have XY's Pokemon availability. You could do three or so different playthroughs with almost no overlapping team members. Then it'd have to have the puzzles and dungeons of Gen II and III. I mean, the Ruins of Alph segment in Johto and the Regi Quest in Hoenn were great. A+ dungeons, too, as I remember getting lost in the Whirl Islands and Hoenn's Victory Road.
We'd also need Johto's and, to a lesser extent, Hoenn's 'events' back. Remember the Bug Catching Contests? And I was pretty damn fond of the Trick House. Unfortunately, never played B2W2, but I hear shit you can do in those was pretty good. The PWT would be a necessity, though, from what I understand. Refresh could return and I would undoubtedly would want Secret Bases back.
Give me Gen V's characters and a map worth exploring like Sinnoh (with elements of Unova and Hoenn). Maybe a few more water routes, but the 'Battle Zone' in Gen IV was close to perfect for me. Mainland wasn't bad, either. Very chewed up terrain when you weren't in a town.
Finally, for postgame, I'd want something to akin to FRLG or Gen II. New areas and such. But also some postgame elements from the current games such as XY, ORAS and SM with more story points spread out over the postgame. Maybe not so 'intrusive' as people say, but still there if you want to experience it. The Battle Frontier could also come back. Don't really care about it either way, but it seems to be popular.