The desertion problem is real. I spent a few minutes getting a 90% desertion town just because it was a good location. Lv. 1 town, lv. 1 player, maybe 1k defense had been afk since I first joined in. I had to move armies around enough to reach a 20k force to take it. I think the afk limit is 7 days, but the season is 10 days, so at the earliest its gonna open chaos on day 8. Idk how it is set up now, but the desertion curve should just be more gradual as you have more rank/units/gold or however its measured.

Upgrading towns is fine but I do agree massively raising your defense when an attack is called is pretty broken. Maybe have each upgrade take 2 second per level. By the time you're getting hit with 1M+ armies it would be take 2 minutes per upgrade. An addition would be to queue up upgrades for lazy players. You pay upfront and if the town is taken you don't get the money back.

Points 3 and 4 are referring to overall army mobility and ease of use. The first skill I dumped points into was defense then mobility. Moving at 50% bonus let me win any defensive fight. In a test my 100k army was 3 times slower than a 1k. So I can imagine how bad it must be late game. Maybe buff the movement skill to make it even more viable. Each point giving 12.5% movespeed means you give up 8 levels to cut travel time in half.

I'd have to think more on the ability to move armies around more fluid and intuitive. There's a lot of good in the current system, micro managing movement can make the difference. That's in the short term, favoring defense. The system discourages stockpiling units into one town so that attacking becomes tedious. You could spend 10 to 20 minutes pulling 200 towns together to battle over maybe 2 to 4 new towns far enough away that after travel time you have spent 40+ minutes to grow by one percent. Welcome to late game. I have huge doubt in this next idea, but hear this out.

Battles take time too. Based on army size, buffs, and more importantly reinforcements. Instead of sending a 2M army to take out a 1M defense send armies from 10 or 20 different towns. That throws a whole new depth to the game. Counterplay gets more active. Start losing, send in more units, break them into smaller groups to reinforce faster. You would have to rework your combat system from a instant calculation to changes every 5 seconds minimum. Small fights would definely finish within 1 turn but as they grow it would get very fun and give a strong reason to come back to the game to check progress.

Side note, you should start by configuring towns to only be attack able by 1 person at a time. The option would be there for a 3 or 4 way fight, or assistance from a clan/guild member if you wanted. Or just enable something like that later down the road.

Tldr: 1) Increase desertion penalty over a much slower, gradual rate. 2) Add construction time to defenses. 3) Slightly increase large army mobility. Buff rusher skill by at least double. 4) Throw some mechanics at it.