Math Overflow and any other "existing" Stack Exchange sites are all Stack Exchange 1.0. According to the SE blog, most 1.0 sites will eventually either be closed down or migrated. MO is probably the most notable exception; as the first and arguably most successful SE 1.0 user, they're a bit "special", so they're not rushing to migrate just yet.
For the most part, you should simply not concern yourself with "legacy" SE sites when considering a new proposal - if you see a niche that hasn't been filled on Area 51, then just propose it. There are already several "migration" proposals for existing sites, like Personal Finance. This is a good thing, it helps to provide a clear path for migration if and when the proposal gets off the ground.