I've only come across three disadvantages of Cool:
1 The compressor is a pain in the ass to figure out. Not even Syntrillium will help me figure it out.
2 It doesn't do some effects in real time.
3 You have to be *really* careful when you're saving stuff, or it'll end up screwed up.
Now, considering how powerful it is, and how cheap compared to other multitrack editors, and how straightforward to use, and how attractive it is, that isn't a long list of downsides.
Cool 1.2 is a very very good program. And for what it's worth, the new version 2.0 (which is about to be released) has real time effects, and if it's better at saving things easily and helpfully, it will be everything 1.2 is not.