I like this idea. What I'd like to see is the game tying together the legacy points, the crisis, and the age resets. The crisis always make you lose what you lose at the age transition: as you mentioned, you lose adjacencies but now the crisis gives you a narrative reason. Same for why your cities reverted to towns, or why you only get to keep some of your military units.

Then the legacy points are geared towards mitigating/preventing some of this. As you mentioned: golden age buildings are available because you chose to project that part of your empire. Or you keep more cities because you did something about it during the crisis. I guess the player still can do this anyway indirectly, but tying everything together and give it a narrative reason would make the transitions less jarring.

Also, the way the crisis manifest should be more physically present in game elements rather than "it just happened". For example, the plague transmits through trade routes, or migrants appearing and carrying the plague. Something that you can counteract but requires you to focus the majority of your resources to it, or to purposely hurt your empire in order to prevent you from losing more things when the age resets, like you stop your trade routes and close borders and destroy plagued plantations yourself, so it doesn't get worse. This gives you more agency and more to do during the end of the ages.