Since my name got mentioned, I'll add my two cents - though doubt it's even worth that.
The problems you mention have frustrated me ever since I first started working with Alice. While there are many partial work-arounds - none are really satisfactory.
However, Alice 3 Beta is now out. Although it is very frustrating at the moment (I've never had it run for over 10 minutes without a crash) - it
does allow you to export to NetBeans (most of the time) - and
once you're there, the crashes (mostly) go away and you have a full Java environment, including many I/O options (including some MIDI play options I've always missed in Alice 2.x).
Starting in Alice, however, does let you set up a nice framework for animation - including mult-thread program setup, something I've never come close to mastering.
I suggest you take a look - and also contribute to the bug/suggestion site. In a posting elsewhere, Gabe describes the why's and advantages of that site.
Good luck.