Seraph started a great thread on all of the plane types that lays out the diffs between 109 models,
check it out. I only have the F-4 and E-3 unlocked as of now but I prefer the F-4 for its greater stability, and speed. Its still a good turner, something lost in later marks, though its armament is less than the E-3. Incidentally alot of Luftwaffe top aces stayed with the E-3 instead of the F-4 because of the armament issue. In Fact Adolf Galland even field modified his F-4 to have the E-3s two outboard MG FF cannons in addition to the F-4s motorkanonen.