I don't think I ever looked at navy in Endless Legend, but I definitely like Civ's naval game.
Here's the thing though: Compared to Planetfall, Civ has several key differences.
- Navy can attack coastal cities
- Ranged navy can use artillery to support land engagements
- Several late-game naval units have unique abilities to further assist in land combat by projecting power
- A deeper roster of naval units to work with
- Embarked land units don't stand a chance against dedicated naval units
The first four are the important ones in my mind. If those weren't true, then navy would be boring, and the last one would just be punishing players for not engaging with a boring system. But because they are true, navy has tactical depth and relevance, and that 5th item makes it mandatory to have a navy if you want to work with water.
As far as I am aware, none of those items are true in Age of Wonders 3 or Planetfall.