Do you think it’s time that Pokemon games got rid of the whole “Team Evil” tradition? It seems that they’re just constraining their storylines a lot more by requiring that every villain be the boss of an evil organization. And I feel like Lysandre, for example, would have worked a lot better as a stand-alone villain.
It sort of depends on how much you value the idea of “Team Evil” as a traditional element of the games’ story, like having a choice of three Grass/Fire/Water starters or completing the Pokédex. Personally I tend to like the idea of ditching as many of the formulaic elements of the games as they can get away with, and I think I more or less agree with your assessment of Lysandre (it’s important to note here that his plan does actually imply the presence of an inner circle that he wants to survive the Ultimate Weapon, but that inner circle doesn’t have to be a “team” in the standard Pokémon sense). I think that as long as they insist on keeping a standard set of elements like this, they’re probably never going to come up with a really excellent story that rivals the best games produced by other companies (either Japanese or western). They can keep improving on their own past efforts, though, and I’m still happy to see them do that.