Endless Legend has some improvements over Civ, but also some specific things that rub me the wrong way; as a lot of the changes I dislike are closely tied to changes I like, I expect this might be a taste thing.

1. Cities automatically work every adjacent hex; population can be allocated to any of the resources at some rate adjusted mostly by the hero governor, and cities can be expanded to be adjacent to more hexes. But there are predefined regions and cities can only work hexes inside their region, and there can only be one city per region- and so many spots which would be great places for cities simply cannot be settled, and settling a region without completely exploring it sets you up for regret later. (This also applies to your starting region!)
2. Heroes have potent effects as governors- but those effects are determined by their traits and race, both of which you have very little control over. You might have a great city placed on a river in a region with lots of river hexes, but not have access to a Broken Lords or Drakken hero who could greatly magnify the amount of dust or food produced by that city, because there's a random set of 10 heroes to choose from in the marketplace.
3. Terrain produces four different resources instead of three (science can come from land instead of people or an offshoot of wealth like in Civ), but hex production tends to be a huge component of overall empire wealth, and so you may have very limited ability to specialize your empire's resources. (If you're in a tundra, you're going science-heavy; and if there's not a nearby tundra, you may be science-deprived.) This is partially offset by the ability to allocate population freely to any resource, and not as bad as it is in Endless Space (a very similar game made by the same people).

It seems like most of the changes from historical / fantasy 4X games are inspired by space 4X games; the regions seem to me to be the analog of planets in Endless Space, the hero system is basically the same, and so on.