Both have their own unique and special drawbacks :-)
AMOSPro+Compiler works well and is very easy to learn and directly implement ideas in. On the other hand it's all hardcoded to suit the A500. There's workarounds in the shape of machine-language procedures, but I doubt it gets you anywhere near something that looks like an A1200 native implementation with real OS support (I might be wrong though since it's been alot of water under the bridge). But if you're just after something that smacks a gui on the screen, does some stuff with buffers and read/write raw output to files then it pretty much works for anything (great that way). It's also good for writing small games (like Scorched Tanks).
Blitz on the other hand supports post-A500 hardware if my memory serves me right (might not). But there's probably good enough reason(s) why people still prefer to use AMOSPro+Compiler. -I've never heard anyone saying they prefer Blitz while having AMOSPro+Compiler too.