The Bf-109's landing gear arrangement was barely adequate as it was. It's not clear how it could have been beefed up given that it had to retract outward into a fairly thin wing. Many Bf-109's suffered collapsed landing gears -- especially when operating from rough airfield in the East.
A better choice would have been the FW-190A. It had a wide-track landing gear that folded inward. Plus, it had a radial engine for ease of maintenance -- an important consideration for carriers. Folding wingtips, similar to the Zero could have been added.
Much is made of German aircraft designs making it to Japan. I guess German pride would have prevented the adoption of the A6M Zero.
BF-109 also had weak wings. A little bit of damage and a tight turn could snap the wing. Wings were also unable to house high velocity 20mm cannon.