When Defer Atmo is enabled (by default in TG4), AA has the most significant on both level of noise and render time for clouds and other atmosphere elements. AA4 or 6 (at most) should be fine for any scene without significant numbers of objects in it. When objects are involved you often need to use higher AA and then you need to start getting to know the "adaptive" settings better to get good render times with Defer Atmo enabled.
The GI in Clouds will affect the quality of the lighting in the clouds, but not the level of noise. I would not suggest changing it. Higher settings will also increase render time further.
Increasing atmosphere samples can help with noise but you have to really be sure that the noise you are seeing is coming from the atmosphere and not the clouds. Often it is in the clouds. Only dark scenes or heavily shadowed scenes tend to have atmosphere noise. You can test it by enabling a small crop region and rendering with your current atmo samples (or default, 16), then increase to 64 as a test. I would *strongly recommend against* atmo samples of 64 for any final render when Defer Atmo is enabled. You will get very high render times. *If* you determine that atmo is the cause of some of your noise, then you should try something like 24 or 32, but not 64. It should not be necessary to use 64 except in the most extreme circumstances (again, this only refers to when Defer Atmo is enabled, and assumes that AA is 4 or more).
Easy Cloud is a new cloud *shape* model that uses v3 shading internally. So the shading qualities should be (potentially) the same as manually created v3 clouds, but the actual shapes, density profile, and specific settings for lighting will be optimized for the specific cloud type. Basically, you can achieve similar results to Easy Cloud with a lot of work setting up complex Density Shader networks for your clouds, and getting the right settings for your v3 scattering parameters (in other words the potential is there in the default v3 setups). But it's easier to use Easy Cloud, which is why we made them.

- Oshyan