I own 3 PRS SE's... a Korina Singlecut, an Akerfeldt singlecut and a 25th Anniversary Custom 24.
Amazing guitars when you consider their cost.
The only thing I don't like about the SE's is the low-quality plastic nut.
But that's all you'd really need to change, as everything else on the SE's is at least above average.
The tonewoods in particular are of excellent quality, as all three of my SE's has a very lively & resonant unplugged sound with each having it's own unique tone (in accordance with what you would expect from the woods used for each guitar).
So as a matter of necessity (IMHO) I upgraded the cheap plastic nut to a Graphtech Tusq nut.
As a matter of personal preference I installed Schaller locking tuners and have ordered BG pickups for each.
After the modifications, I much prefer my PRS SE guitars to any other guitar I own or have owned in the past, including my Ibanez PGM301 and an Ibanez JS1200.
And they still cost me far less.
Here's a link to some more detailed info in a previous thread of mine:
http://www.rig-talk.com/forum/viewtopic.php?f=3&t=73406