I've got a squire telecaster custom (rip off of fender tele deluxe) I got some cash and want to make the guitar a little better for some alternative rock (pretty heavy overdriving amp)
here's what i'm thinking;
New bridge pickup (Alnico 2 maybe)
new tuners (Grovers)
new bridge saddles (graph tech)
all new pots and toggle
MAYBE a new neck (Warmoth)

any other things i could do to make it better?
How much are you looking to spend? Depending on your budget it might make more sense just to get a better guitar. The more the better I say.
Slap a humbucker in that hoe. put like an evo in the bridge.
ESP Eclipse Standard Series W/ PRS Santana II Pickups
PRS SE Soapbar II
Peavey 5150 120w Head
Avatar 412 Traditional Cab(v30's+G12H30's)
Malekko, Rocktron, T-Rex and MXR/Dunlop pedals