I originally wrote this in the Shichibukai thread, but felt that it would be better if it got a thread of its own. Anyway, here's my two cents' worth:
Has anyone considered that 100 million is a damn huge sum? Imagine if you got 100 million dollars. You'd be fucking rich, that's for sure. Hell, you'd be loaded even if you got 100 million mexican pesos.
Now, the government doesn't have infinite amounts of cash, and because they give out a bounty for nearly every pirate it can become very expensive very quick. Therefore, the government might feel like 100 millions is enough incentive for bounty hunters to go after a pirate of Luffy's caliber.
In short, what if the government people are cheap bastards who don't want to pay more than what is absolutely necessary? This would explain why some bounties seem to be lower than they should.