Try to make your device modular and use one NXT per module. This is easier to build, develop and test and thus, more fun. Use as many motors in a module as you need. But don't forget to look at other possibilities as well. Gearboxes can be used to drive different functional parts, but only one at a time. Touch sensors or light sensors can replace tacho's sometimes. Connect the modules over a network. RS485 seems the best solution for time synchronized networks. While you have two NXTs you don't even have to use custom cabling (I guess).
In the meantime, I purchased 2 more NXT bricks which gives me more freedom, but doesn't make it more easy.
I think I will now, setup a RS485 network, and use motor multiplexers on each port, this must do the job. Once I get it running, I hope being able to get back in here and share my experiences with you.