I recommend new strings, and a good setup, make sure the relief is minimal and the action is nice (I always go for less than 2mm @ 12th). Also, you may need the nut lowered slightly on the E side but get a luthier to check that.
Also, I know this sounds lame, but make sure you're not fretting too hard - that can really knock the intonation out.
I second the above post that Fenders factory setup isn't exactly optimal. I mean, it's ok for most I guess but for us fussy folk it needs a decent amount of tweaking. I had to restring mine, adjust the truss rod, set it up nicely, and I still wasn't quite happy - I ended up putting a very thin shim in the neck pocket! It's perfect now