Hey Nima, my comments:
1. completely agree
2. There's a brand new package, dotlrn-catalog which will help to address some of this issues, its independent of .LRN (so you can have you own course catalog), and can be tied to .LRN, a future enhancement will be to get rid of the rigid structure of deparments -> subject -> class, which in real life does not fit all the needs, and use the dotlrn-catalog, and from there address your suggestions.
3. Yes, LORS will change, we had the same difficulties and some work is going on to make it more flexible, I'll let Ernie to answer this question...
