They definitely need to expand the war model. The current system is not working. Straight glory matching would work, but ensures that only teams with mostly high atomics filters to the top - the transition period would be brutal. It would end sandbagging immediately. Teams that pay to win would mostly end up playing each other at the top. Win-win for them getting the most glory, and the rest of us not having to face them.
Another set of options that I think go well together:
Limit the war size options. 10,20,40 would be good steps I think. Then there aren't as many different pools of players.
Multiple wars at a time would be a great complement to that. Then a full alliance can have two or 3 going at once.
Only allow a range of three ages to be included in the war - you pick the ages, but if you have an atomic then nothing below industrial. Have a different war for the Medieval / GP / EA group. And you can only match against teams with the same top age as yours.
Do all of those at once, and there are a lot more war teams in fewer pools, with better age segregation and fewer brutal mismatches possible.
On top of that, I suggest having a few specific times of day that wars are started - every 8 hours, take everyone in the pools, make the best matches you can. If there is a leftover team, guarantee they will match at the next time period as the first choice to be matched. Adds predictability for when wars will be starting, and you can start right before one matching period, and be guaranteed a match within 8 hours and a bit.
And separately, to encourage more people to participate, improve war loot. Start by giving out as much loot as you would get in a mp attack for each war attack (in battle, replace the piddling numbers there currently with 2000+ oil minimum and 400k+ food/gold for a global, and 3000+ oil/500k+food/gold for an atomic). If you do that, then the war loot you get at the end of the war doesn't need to be changed too much to allow war attacks to at least cover their costs.