Well, Krusty...Ya gotta look at it this way. Bf-109 was designed in the late 30's. It was built according to the existing aerodynamic trends of the time. If you'll notice, alot of early war planes had similial fuselage shapes(High ventral area in back of the cockpit, Spits, P-40's, early P-51's, F4U's, etc.) and the wings were built with a chord and profile similiar to a racer's.
Add to this, Dipl. Ing. Kurt Tank, and Willy Messerschmitt were two different designers with different schools of thought. Willy did build a completely different fighter, the ME-209, with tricycle landing gear, bubble canopy, low-tail fuselage, as a follow on to the 109 series, but it wasn't procured by the RLM. It wasn't seen as being enough of an improvement over the existing 109 series to produce.