Here's just the thing....a set of studio monitors or high end bookshelf speakers are technically "better" speakers than the 2.1 Klipsh or Logitech sets. But to a large percentage of the buying public they don't want "better". They want louder. The 2.1 systems have an over boosted mid/bottom end with very large subwoofers filling in what the small satellites can't. It's a muddied, overly loud bass. But you can feel it, hear it, and it rocks that house. That's what many people *prefer*.
Studio monitors in this range like the M Audio AV-40's can somewhat hit the bass levels of the 2.1 systems, but no where to the volume and depths of the subs.
Plus a lot of the studio monitors are really large, ugly (think 1980's looking) speakers. They take up a lot more desk space than a small satellite and sub you can cram under your desk.
"Better" is a relative term. If a studio monitor sounds thinner than a 2.1 system to someone who likes over boosted low ends they aren't going to say it's better.
I'll be honest, for basic listening, games, and rock/metal music I prefer to use my 2.1 cheapie computer speaker system with the big ass subwoofer. But when it comes time to sit back and listen to some very mellow, blues, jazz or acoustic stuff I'll flip over to high end stand alone speakers.
For somethings I like the over boosted bottom end that the low end systems provide. If I want to sit back and enjoy the imaging and beautiful reproduction of music then I'll move over to the dedicated speakers for that. But 90% of the time it's the 2.1 set that's in use.
For your budget a true bookshelf system + amp to drive it isn't going to get your very far and it's going to likely sound thin compared to a 2.1 system or lower end powered monitor like the AV40's.
Last week Best Buy had the Klipsh Promedias on sale for $100. You really can't go wrong for the money with a setup like that.