Well, here's what I've read and seen...I'll post the thread if I ever find it again.
First of all, the physical location that you have to place the aftermarket HU in sucks--it has to go in the top center on the standard HU/tape deck combo, which is about where the wooden door is right now. The wooden door has to come off, or stay up all the time--it can't be pulled down because due to the depth of the cavity behind the dash the HU will stick out too far to close the door. Secondly, the whole reason it has to be in the top portion that the bottom part, where your primary radio controls are now, is way too shallow for an aftermarket HU.
In addition to all that, the BMW units are a lot wider than aftermarket HU, so you have to find 1) a bracket that will fit, and B) a filler faceplate to go around your aftermarket HU. This is where it looks ugly. I'll try to find the pic I saw once.
And, like I said, you loose your OBC controls--you'll never be able to reset your average MPG, trip time, speed alarm, etc.
EDIT: Here's the picture of an aftermarket standard size head unit installed in an E39. It looks like a gaping hole was punched into the middle of the dash and then a bunch of cheap plastic was used to fill it in. I admit that's probably as good as it gets when you do this on an E39, but seeing that much empty plastic makes me think of a Cavalier or something. Hopefully you'll be happy with the new speakers and subs. What would you use the LCD for anyway? This is supposed to be the ultimate driving
machine, not visual entertainment machine!
No offense intended... I'm sure you have reasons, that's just not my thing. Anyway, I hope this info has helped.