As an "old school" top-down-design, step-wise refinement (did I age myself enough?) kinda person, I'm dealing with just this issue myself for a site I'm about to re-launch that was somewhat successful in its niche.
I do truly think that the mega-community sites will be few and far between, and that niche communities will develop organically. By that, I mean that the first thing to keep in mind is, well, the community that will be served. Then, look to the existing mega-communities for features that may serve you well.
For example, one site I'm finishing up was developed for a film student who wanted someplace where she could seriously upload and discuss film, music, etc. YouTube just isn't the kind of environment for that, but YouTube did have features that she needed. The resulting site springs from that specific need.
In other words, you have to understand the community (group, fans, teachers, paintballers, etc.) first, and the resultant site should be a reflection of what that community needs - "micro-sites" if you will that are fully featured but focused. How "wide" you define your "community" will be dependent upon whom you are trying to appeal to.
This approach will also hopefully make these kinds of sites a bit more economically feasible for folks - hey, not everyone is going to receive multi-millions in "Angel funding".
My personal usage patterns follow just this creed. You can find me across several technically-focused forums, but I've never posted to Facebook (though I have an account) or Twitter (which I simply refuse to join). "Fit, Focus and Function" are my mantra.
Of course, this is a bit over-simplified, but so far it works for me.