Probably Shaymin of Gen IV, because Johto is a green region, not too cold or to rugged. A new Legendary is too farfetched for now and it would be stupid to add another legendary right now, but it would not cause incompatibility with D/P/Pl because they could ban that legendary from wifi & the top of the Pokemon Center like they did with G/S/C. Gold, Silver, and Crystal were compatible with G/R/B/Y and yet Johto contained 100 MORE Pokemon than Kanto in G/R/B/Y.
Oh, and probably Celebi if Gen 2, as it is the Final Pokemon of Johto and it is an event Pokemon.