I don't think the two party political system is all that bad. In many countries, too much political fragmentation leads to stasis, as the government tries to appease everybody by doing nothing. That, and political extortion - smaller parties selling their votes for their sectorial good, and against the greater good. It happens all the time in other countries.
Think of the US political system as a shit filter: rough shit goes in, smooth shit goes out after vast filtering.
Anyway, the nicest solution would be granting the states additional independence. Over time, states will take evolutionary directions until they are differentiated enough, and population will shift accordingly. California could ban heterosexuals and gasoline operated vehicles, for example. It's very difficult to do such massive shifts on the national level, but on the state level it will easily work.
Establish minimum federal requirements from the state - in terms of debt, for example - and have the US act like a a more homogeneous European Union. Have the federal government support the weaker countries through development plans, just like in the EU.
Then it'll be a truly wonderful nation, with everybody finding their spot eventually, and much more dynamic, community oriented politics.
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