I think it is good that casual, lower-level players can get at least one elite pokemon fairly easily, although I agree with your ethic of having more variety in gyms. I have plenty of Vaporeons that make pretty good defenders, but if a gym already has a couple of them, I try to put in something else.
On the bright side, the preponderance of Vaporeons makes my grass pokemon some of my most-used and favorite team members.