Why use discrete Ethernet transcievers?
If your MCU has an ethernet PHY built in, you would normally use that.  But many MCUs do not have that available.  Even so, here are several reasons I can think of why you might not want to use an internal PHY.

1) Design reuse.  If you have a previous design that used an external PHY (perhaps on an earlier MCU that didn't support an internal PHY), you may save on development time by using the same design and code.

2) Physical separation.  You typically want to put the PHY as close as possible to the magjack.  If your MCU has to be far from the jack, it may make sense to run the MII signals across the board.

3) Different physical medium: you might want to use a fiber optic PHY, either as standard or an option.

4) No PHY: For short-range communication (say between modules in a single chassis), you can even skip the PHY entirely and connect the RMII signals directly. In particular, if you are making something like a SOHO router, the on-board MCU might connect to the switch this way, avoiding going through two PHYs.