Constantin:
If all you want to do is program a 1284p then a $10 chip and some bits and bobs and a breadboard will put you in business. But the main reason that folk get Mega's, 644's and 1284p's is lots of sensors, I/o devices, etc. and their attendant libraries. That's why the bahbot, Bobduino, and Brewtroller have so much to offer on their boards.
Sure. They have so much to offer if they stuff they have is what you want. The reason Arduino itself is so handy is that it leaves it completely up to you to decide which sensors are for you.
Bahbots and Brewtroller are special-purpose boards tuned to do something specific. In that case, you'll have exactly the needed parts because it's purpose-built. For general use, having a 1284P-based mega jr. would be just what the doctor ordered.