I often wonder what stunted the P39, and latter the P63 development programs. Bad management, back room politics, poor engineers or all four. Loosing both P63 prototypes suggest bad design and bad management.
The removal of the turbo supercharger as already mentioned was probably the single biggest blow to the P-39, but there are other aspects of it's design that would have limited it usefulness in US operations during the war.
The reasons behind the removal of the supercharger seem to have been largely been a combination of finances and optimistic thinking, the turbo supercharger reliability was still in question during the development time of the P-39. Companies typically didn't get paid till a production contract was awarded and the delay in production may have bankrupted Bell Aircraft, they also had wind tunnel data that suggested that the P-39 could still attain 400mph w/out it. I'm going from memory, but as I recall those were the primary factors behind the decision according to the book "Cobra! Bell Aircraft Corporation 1934-1946" by Birch Matthews.
The most notable other handicap was probably the lack of range, but I also don't think the armament was ever entirely satisfactory. The 37mm had a really low ROF and low muzzle velocity, and the combination of cannon, .50 cal, and .30 cal weapons meant you had 3 different ballistic properties to contend with. The 37mm was also plagued by jamming in combat (at least in the south and southwest pacific).
The flight controls were very, very sensitive and responsive which is where you see praise for the handling from the likes of Chuck Yeager and Bud Anderson, in the hands of a skilled pilot the thing must have been a lot of fun to fly at low altitudes but a more average pilot would have had their hands full. The P-39 had a wicked accelerated stall that would bite the unwary.
