I've long thought about ways to make CN better, and my two biggest gripes are in actual nation-building.
1.) I'd like to make wonders more tied in to actual game mechanics. For example, you need to buy the Internet to get past 5,000 infrastructure. Or you need an Interstate System to get past 3,000 infrastructure. And things like that. Obviously there is always infrastructure for nations (in RL) to enhance, but it usually goes towards specific things. (For example, there are only so many dirt roads a nation can have, in RL). So, tying the wonders in to game play, would change how you build your nation. And at least momentarily make CN more complex... until someone figures out the optimal way to do this.
2.) Have stockpiles for alliances. (This specifically comes into play with the new projects implemented in TE which allows alliance leaders to kick people from their AA and stuff). Basically, it'd be a system that would help recruiting alliances that would work something like this: For every bank your alliance has, you have $1,000,000 in a stockpile that can then be distributed to anyone in your alliance once every 90 days. So, for example: Ragnarok has 485 banks. Every 90 days we have 485 million to be distributed as our alliance gov sees fit. It takes up no aid slots, it just goes to wherever they assign it. Similarly, Barracks would provide 500 soldiers per improvement in the alliance. All transactions must stay inside the alliance however. So Ragnarok can not give 300 of it's 485 million to FARK. Different improvements provide different resources to the stockpiles. Wonders contribute even more. (Numbers are just for example purposes, and would obviously need to be tweeked). This adds a new dynamic to alliances, and would certainly add more strategy to wars.