This is known as Duverger's Law:
http://en.wikipedia.org/wiki/Duverger%27s_law
There are a number of meaningful counterexamples, perhaps most notably in the UK, where Lib Dems have received a significant number of seats since 1974.
These discussions tend to obscure the degree of differences within a given party in the US. (ie, Zell Miller and Dennis Kucinich once shared a party. Though Kucinich was given an "F" by the NRA on gun issues, Zell was later elected to the NRA's board of governors. Kucinich was also a strict vegan, while Zell once threatened to shoot Chris Matthews. You could run similar comparisons by bringing in other Dems, you could do the same on the other side of the aisle. ie, not many Republicans would consider marrying one of the Kennedys or praise Obama's post-hurricane support, but a couple would.)
Any two-party system with a diverse electorate will eventually have to allow substantial variation in candidates and viewpoints, or it will be inevitably reduced to regionalism and obscurity.
A many-party system will eventually force smaller parties into large coalitions to attempt any governance at all.
In short, a two party system and a many-party system are not substantially different in the number of political viewpoints they entertain, nor in the types of compromises required between those factions to result in political action.
If you're not already aware, I would encourage you to check out Lawrence Lessig and the Rootstrikers organization which is aiming to reduce the influence that money currently has on elections.
Question: Can you recommend any particular organizations that are employing your above strategy of targeting primaries of contested districts to defeat soulless "bought and paid" incumbents?
But you can get the result you want through the primaries. Run your candidate against the incumbent in the primary and keep emphasizing your specific issues and publicizing the incumbent's corrupt stance on them -- even if you don't always win, you may be able to get the incumbent to change positions.