One thing I've noticed about my new tele is that at the lower frets if I push down a little hard the note goes sharp. It seems that the frets are big enough and the string gauge is light enough (.09) that there isn't enough tension to prevent me from bending the strings when I push down. Would stepping it up to a set of .10s help to remedy this? Seems like the easiest route before ditching the neck for one with smaller frets, getting it refretted, or relearning 12 years worth of technique.
.10s worth a shot?