First, based on your options, I'm assuming you want to stick to SkyTeam? There is also a Swiss flight from JFK to Geneva, but I assume you're looking at the Delta one (it's relatively new and I've not taken it). There are very few direct flights from the US to Geneva - the two from JFK, UA from EWR, and UA from IAD. I've never traveled from ATL to GVA, but I've traveled from other US/Canadian cities.
I don't hate CDG as much as others on this thread. With the egates for passport control, it often is pretty quick (and I've seen AMS super backed up for passport control, so I don't feel that ether one has the consistent win there). Between the two (AMS and CDG), I generally go by which is cheaper/has better timing. Also, CDG used to have a gross lounge in the F pier (from which the Schengen flights leave) but now it is really nice.
Depending on your gate for the US flight (all Schengen flights leave from/return to the F pier), you can have an annoyingly long and convoluted walk (with or without a bus or train) in CDG. In AMS, it will just be long. CDG is well signed, but can be convoluted with random ups and downs (and trains or busses).
Agree that connecting in Europe avoids having to do US customs/immigration during your connection but you'll have to do your exit passport control during your Europe connection (though you won't have to pick up luggage).
Geneva can be really hit-or-miss on passport control for non-EU/non-Swiss passport holders. I've seen lines of an hour but also seen super short (i.e. as fast as you get can to the front) but generally middling. There are no e-gates for US passport holders (though things may have changed since I last flew in last October). Luggage generally takes forever, so skipping passport control (because you cleared elsewhere) can just mean a long wait at the luggage carousel.
In terms of the airlines themselves, I find them pretty similar though I sometimes base my choice on the aircraft itself (usually I'm in business class and the seats can be quite different).
I like at least 2 to 2.5-hour connections in those airports (though it depends on the direction I'm traveling).