Chords are for people who aren't cool enough to get a rhythm guitarist to play behind them.
I don't buy the "CAGED System" as such - I mean, no matter how your guitar is tuned you're still going to get a stock set of chord forms. They just happen to come out to nice round open chords, in standard tuning, rather than like Bb's and F#'s - but the basic idea is sound, that you should be able to play a bar chord form of any open chord you know. Play with that for a while before you dig any deeper, getting comfortable with D-shaped, C-shaped, and G-shaped bar chords, in both major and minor forms.
Then. once that's comfortable, spend some time getting a feel for the major and dominant 7ths, and then try adding and removing notes - sus2's and sus4's, add9 and 11's, b5's, whatever - and have fun with little Jimi-like agumentations a la Little Wing.
You do it right, and the idea of chord forms should sorta deconstruct on itself, just leaving you with a bunch of notes.
A great place to start, though, is by making yourself a human capo - take a progression like Am-C-G-D, and then play it in Dm, at the 5th fret. Aside from just being a great comping excersize, this is an invaluable skill to have if you ever find yourself in a gig with an acoustic guitarist who likes using a capo. I played with this blues-rock band for a while, great group of guys, but we never had a "set list" per se, and every once in a while the vocalist would grab a capo and start playing open chords in a really awkward position on the neck. Your hand will kill at the end of the set, but it's a lot easier to play chord shapes you already know barred a bit up the neck than work out what something like the above progression should be with a capo on the 6th fret, on the fly...
-D
