[0] https://en.wikipedia.org/wiki/Atmospheric_super-rotation
If you're floating you don't have to track the ground.
The difference is in air pressure and gravity.
Gravity means comfort for astronauts. It also makes, I suspect, science and industry a bit easier.
I don’t know what air pressure means. Spacewalks probably get easier. But now your structures have to deal with aerodynamic forces, which is annoying. Making up for that, you’re suspended in a soup of precursors and reagents—that opens up ISRU possibilities. And you should be getting less radiation in atmosphere.
On the whole, if you’re doing planetary science, I think being in the atmosphere is hard to beat. If you’re doing any industry, being near raw materials beats shipping anything unprocessed out of a gravity well. So if you’re staying for a while, you dip in. If, on the other hand, you’re just visiting for a few days, yeah, take a lander and then get back out again.
How would that work? Averaged over the planet, you get half the year in darkness and half the year in light. There's no other option.
We have that same ecosystem on Earth.