The only way to halt stagnation is to create conflict, and to create conflict, we need, as Heft said, scarcity. Master-Debater has a great idea with the land scarcity thing.
Create a set amount of land on Planet Bob and make it more profitable to have more land, e.g. you could make it so that you need a certain amount of land in order to build an improvement or wonders.
Changing the war system wouldn't really change anything, except for the strategies used to fight. It would do absolutely nothing to reduce stagnation. Likewise, changing the aid system or anything to make it easier for smaller nations to grow still wouldn't change anything because, no matter how you change it, the older nations will have an advantage. Capping infra, tech, etc. is a terrible idea, too. It's unrealistic and would just make it boring once nations reach the caps.