Actually, the #1 advantage to using MAMP is tremendous: Each time you upgrade your system, your environment won't break!
There were a couple of Snow Leopard updates (or maybe it was Leopard to Snow Leopard, I can't remember) that broke Mysql. One was by moving the mysql.socket file. There was another update the broke PHP. In both cases I had to hunt around the Internet for hours to find obscure sites with info on how to fix them.
With MAMP you don't have this problem, you can install all your OS updates, or even wipe the hard drive and install from scratch (provided you make a backup of your MAMP application of course) and still have all your environment just like before. This is the main reason I use MAMP. I've been bitten by these problems too many times.
When compiling new stuff, you have to make sure you tell it to use the MAMP files and not the built-in ones. This can sometimes be a problem for some Rails bits (Phusion Passenger gem comes to mind that complains about not finding the apache sources). But depending on how much tinkering you are doing, MAMP is a godsend.
With regards to having stuff duplicated on your drive, the solution is very simple, just delete the builtin installations that bother you, I got rid of /usr/local/Mysql to avoid conflicts. Though I wouldn't recommend deleting apache and PHP.