Objectively, 3.0 /.02 Falcon was proably the best. Had old "bugged" throw release points and Uthrow timing which was more favorable to Falcon. Pretty sure air Side B was true spike back then
Subjectively, 3.6 Falcon is the best because other chars got nerfed from 3.0 . Falcon was outshined by stuff like old Mewtwo, old Mario, etc. Similarily, patches even older than 3.0 are probably in a similar boat due to chars like Lucario / Sonic / Ike
Falcon is mostly the same throughout patches, but other character viability has a huge impact on him. He has had many formerly hard MU's or outstanding character threats nerfed over time. This matters more than whether his Side B spikes vs meteors, whether Uthrow has 2-3 more frames of lag, etc