The historical reason for missiles not dominating is friendly-fire. One should not be able or willing to fire missile in a melee due to fear of hitting own units. Missiles should be for skirmishing and harassing.

Technically at some point someone planned for walls to upgrade to fortresses.

Since 0ad is a historically-themed (if not historically realist) game, the way missile work as of now (being the main weapon) is really bad and harming the gameplay a lot. What are the solutions ? What is the role that we want for missiles and how to do it right ?

Especially since walls are heavily underused in the game now, as some already pointed. And that's a shame ! Walls are historical and should be fun to play. Maybe remove the fortresses and have a "dungeon" building instead (yes, dungeons are the wrong historical period, so use the historical one, but I don't know its name) that can't work as a defense without walls ? So the actual defensive structure will be much more varied, and tactically interesting ? And of course change the way soldiers fight on walls, so that they don't die immediately from enemy missile (except from missiles on siege towers, obviously), which is the reason nobody garrisons units on walls as of now.

Use it yourselves.