The issue with Venus and Mars is that there is no magnetosphere. Over geological time periods the hydrogen is slowly lost into space. All that CO2 in the atmosphere could become H20 given enough introduced hydrogen, and photosynthesis.

It would be a colony constantly depending on Earth supplies and you would be constantly rebuilding it. Just like every other planet, nothing can permanently survive in upper atmosphere. It would be easier to have a massive ISS-style station in orbit, with a tethered cable elevator for research.