the deep elves were gods. they were great at magic as there constructs prove, they are powered by soul gems probably some really powerful conjuration spell. they were geniuses as there understanding of the universe and technology proves. they had a gods heart that just proves there were amazing. they were also arses since they did enslave a pretty powerful race, snow elves, but that proves they were great in military matters. so pretty much they are perfect which makes them gods, and they left the mortal realm for a better one more fitting for gods.
You seem confused. I'll go point by point.
Dwemer were not gods. They were pretty good at magic. Their constructs were not conjuration spells. They were indeed geniuses.
Having dominion over a god's heart doesn't prove that you're amazing; it means you're lucky enough to have found it. Which they would not have been able to do without the Chimer.
They probably weren't that terrible at military matters, but great? They only reclaimed Resdayn from the Nords because of Chimer aid, and there are not many ways to interpret the events of Red Mountain without saying they lost, or alternatively had a pyrrhic victory. Nor did they enslave the Falmer through warfare. The Falmer were looking for an escape from the Nords, as Dawnguard says.
They did not go to their own plane of existence, befitting gods. They turned their souls into the skin of Numidium, which is a Walking Way. This is to say that they did build their own god, and used themselves to finish it. But they never activated it.They probably don't really have a "sphere of influence" since Numidium is gone.
The Dwemer were cool. They were not perfect. Even if they were, that would not make them gods.
Some sources:
http://imperial-library.info/content/nerevar-red-mountain
http://imperial-library.info/content/morrowind-secret-song-truth-red-mountain
http://uesp.net/wiki/Skyrim:Knight-Paladin_Gelebor
I unfortunately can't remember which text confirms what happened to the Dwemer.