Part of the problem with the no war penalties of stagnation is that it takes me months to save for a city. Assuming I sold every resource I made it would take me over 3 months to save for a city. I still have to have save resources and cash for a war chest. I am only at 43 cities. This combined with the having over the city average penalty is going to stagnate growth a lot.
I bought the military research based on what it provides today. If it is going to provide less it needs to have a reduced cost by the same percentage. Maybe a refund to early buyers.
Spies need to be reworked. I have all of the spy projects and would like more offensive capabilities. Or at least more spy operations than 2.
The recent stagnation was created by the development staff and military research. It has taken time to buy it. The summer is usually slow in the game anyway. At some point stagnation penalties would end up being permanent. I don't think the last 40 wars I fought would get me back to zero after a 120 day stretch of peace.