I think Kixeye had some good ideas for War Commander, but I think they should have stuck with the original concepts when the game was great. As a person who likes traditional real time strategies and plays Command & Conquer a lot, I have some of my own ideas.
I was thinking that instead of building just one base over a long period of time in one sector, players should get to quickly build a base every time they log in and on whichever map they want to play. Every build time should be quick like it is in the mobile game Rogue Assault. As for the prize units, I think they should be unlocked in a permanent tech tree to be used in later skirmishes. Remember the old events in 2012 and 2013 before the event shop was created? That is what I am thinking about here.
What I described is Command & Conquer 4 but with a War Commander theme to it: post-apocalyptic Earth. I think that would have worked better. Each time they win a skirmish against AI factions, they gain some experience and can buy new toys with the exp points. There would not be any deposits to capture; only bases to hit for experiences and resources. That is how I get resources; I fight for them.
I think this would have been a perfect design choice. For new players, they should have started from the first event in the game's history and worked their way up to the present time. In my opinion, this would have fixed my problem with internet connections. I do offline skirmishes in my free time and little to no online play. No world map required, so the game would have been just like in early 2012. That means no hunting for bases either since players can choose to make enemy bases appear when they start a new game.
For me, playing a game is about giving the players some control so they can have fun. What could be more important than having fun? That is why I play games. I left War Commander because I felt that there was a lack of control: I had to play events at specific days and I was paranoid when my base was being attacked in a sector. I hated how powerless I was. Instead of being harassed while I was sleeping or running errands, I should have arranged a PvP fight that both my opponent and I could agree to. Not only would I not be angry at them and at Kixeye, but I could have had fun. Maybe I overreacted and took War Commander too seriously, but I try to live a decent and honorable life.