Hi codefox,
you started this topic to seek some advice and it ended up more the other way around. :)
I frankly do not know anything about Lego (I only played with the Mindstorms NXT thing for a while), but my friend asked me if I would be able to come up with a Bluetooth replacement for the IR Lego remote and since I was already looking forward to play with something that uses wireless transfers, I started to think about it in my free time and came up with essentially the same thing you did -- and few days later, my friend found out about this topic.. :))
I'm going to use the HC-06 as well, but a different driver chip (DRV8833, the one in V2 PF receiver, since it basically seems to be the only one with reasonable parameters and availability in my country..) and a PIC16F1508 for the MCU, since I'm aiming for something more like an universal Bluetooth remote control "platform" (so I can simply use a scaled-up version with the same FW/HW to control lights or other stuff at home, make a 4-motor version, provide feedback from various sensors or whatever.. ) and even though I like AVR's more, Atmel just did not not have the right chip for the job this time (or maybe they do, but not available in Europe again, oh well..). Oh, and I'll probably use your lovely Android remote if you don't mind, no reason to develop that twice, right..? ^^
I'm still several steps behind you, but I've received my Bluetooth modules just today, so I'll build something up in the following days / weeks (not much time for "hobbies" unfortunately..) to test my circuit and then proceed to the PCB design (I don't think I'll manage to make it so small, it is only my third non-trivial design (+first SMD-based) and my primary manufacture method is still toner transfer so I'm running into the same vias issues as BrianZ ^^). I definitely want the polished-up later boards to be complete with solder mask and silkscreen, but the local manufacturers look quite expensive for small batches / samples (so I never even tried to get something manufactured) -- the OSH Park seems really great for this, thanks for the link..
I really wonder what comes out of this, (in both cases ^^) I just hope my DRV8833 does not burn-up on the first try as I don't have anything to use for soldering the thermal pad.. :D (guess some thermal conductive paste will have to do..)
Anyway, thanks for sharing all your experiences, I may find them useful as I continue. :)