You don't have to agree with them 100% to believe in them. I don't agree with Gary Johnson 100%, but I do believe he would do the best job (hence "I believe in him" and thus my vote is not wasted on Obama or Romney). You say you don't agree with Obama 100%, but do you believe in him? Based on your statements is sounds like you do. Good for you. You're voting for a candidate you believe in (and thus aren't wasting your vote).
Those Libertarians that used to be Republicans did try, you might remember that Ron Paul had quite a lot of support from voters... Until the Christian Fundamentalists stacked the deck against him. Several caucuses (like St. Charles, MO) tried to over-rule the crowds in attendance and send delegates that supported the "chosen" candidate at the time (usually Santorum or Romney). Those where Paul did win, and got delegates to the National Convention, found that the Paul Delegates were getting kicked out and replaced with pro-Romney delegates to limit dissent within the party. At one point in the RNC they stopped putting the numbers up for Ron Paul. It's difficult to retake a party when your opposition has themselves so deeply entrenched that they can change the rules to be in their favor.
Not all Libertarians are disenfranchised Republicans either. Some of them do believe that the role of Federal Government in our daily lives should be quite small. That maintaining a strong military is important, but that we shouldn't be as aggressive as we have been. That Corporations do *not* have the same rights as people. That Religion, Race, Sexual Identity, etc.. should play absolutely no role in legislation (ie: legislating who can and cannot be legally married based on the religious definition of marriage). That Marijuana should be legalized and regulated like Alcohol and Tobacco (the side effects of which are reduced prison populations, reduced power of drug cartels, more tax revenue for states... all of which would be fantastic for this country). Most of those views (despite being a truly "conservative" view-point) are the opposite of anything heard from the Republican Party during the last 50+ years.
It's also an arguable point that if the Libertarian Party wanted to change the Republican Party from within they would first have to prove that they are more valuable to the Republican Party than the Religious Fundamentalists. If the Libertarians cannibalize enough votes from both parties this election. It makes it clear (to both parties) that they will need to make platform changes and if they don't they will continue to hemorrhage voters over the next few election cycles until the Libertarians or some other Third Party become legitimate contenders. IMHO this is the true role of Third Parties in a Two Party system. They exist to keep the "major" parties in check.
Neither the Democrat Party nor the Republican Party existed when our country was founded, so at one point in time they were both "Third Parties". The Republican Party was founded in 1854 (78 years after the Declaration of Independence) as a bunch of anti-slavery activists. The Democrat Party evolved out of the Anti-Federalist party which originally favored similar views that modern Libertarians have (limited Federal Government and pro-State's Rights). If you look at the history of our country, the idea that our country was designed to be a two-party system is patently false. The current major parties may have changed the rules to be in their favor, but a "two-party" system was never the original intent (if it were the Constitution would probably say something about it).
