Obviously Ottawa or Halifax style amalgamation incorporating rural areas is dumb. But balkanizing a metro area, thus making metropolitan governance and planning much more difficult, is even worse.
I really do not see what is wrong with the amalgamation of Toronto, for example. The only argument I've seen against it really is that it was a plan to gerrymander the city conservative--but considering that greater Toronto is a right-wing area, that's sort of tough luck. Toronto (and in this sense I include Pickering and Oshawa and Scarborough, which are as much a part of the city as downtown) is a right-wing city.
Two words: Rob Ford. Also, Mel Lastman, and now John Tory. Toronto is an extremely polarized city. It has no business being amalgamated as one municipality.
Again, these conservative voters are what the average Torontian wants. Your position is a bit like someone who wants to carve up Idaho so that the Democrats in Blaine County can elect a lefty--except Idaho is a much less logical entity than a fully amalgamated Greater Toronto.