From a lore perspective, I think the Dwemer are more interesting. I find them fascinating. A whole civilisation vanishing seemingly overnight is deeply intriguing, especially when that society was vastly more technologically advanced than their contemporaries and any civilisations that have followed them. I love the contrast between their scientific and technological superiority and the disturbingly dark and ominous undertones to their practices and treatment of other races. So often in sci-fi/fantasy futuristic societies are painted to be more advanced than the more primitive societies in every way; technology, morality etc. But not the Dwemer. They were, for the most part, a race of sociopathic mad scientists. It's refreshing.
There's less mystery surrounding the Ayleids. There's still mystery there, of course, but its much easier to paint a clear picture depicting why the 'wild elves' likely disappeared. They were consumed by their own destructive culture and the wrath of the creatures they enslaved.
From a moral perspective, I prefer the Ayleids. It seems that some of the city-states (those dedicated to Meridia for example) were less oppressive to their human slaves (and even supported Alessia's rebellion) than the more nefarious cultures centred around the worship of gods the likes of Molag Bal. But really, to Godwin up the thread a bit, trying to figure out who between the Dwemer and Ayleids were more good is like trying to decide whether the SS or the NKVD were the nicer group...! I know that's not what you asked for, but, yeah.