I've put in a lot of game time with FE now and I find I really enjoy the game up to a certain point - then I could care less what happens and so usually start a new game. This concerns me greatly because since the first couple of games this has been a regular feeling I've had. Mind you, this is still a very good game but replayability will be a casualty.
The start of the game has interesting strategic choices but by mid game it has become a 'rinse and repeat' exercise which is really boring strategically. I was very critical of the fact that War of Magic was more about process than about choice - and unfortunately Fallen Enchantress also reached this process-driven stage as well by the mid game. And the larger the map the bigger the problem.
The two problems I'm referring to are:
- The champion 'stack of doom'; and
- City spam micromanagement hell
Before looking at these issues, let's recap on the portion of the game that is enjoyable that leads to these problems.
At the start of the game your location has both opportunities and threats. Depending on what monsters will spawn near-by you need to decide how much you can explore or whether you need to hover around home base. And if there are nearby resources this will drive what you research and what you will build in your starting city. Things start slowly but that's OK because this first phase is all about exploring your surrounds and recruiting what champions you can as well as completing quests to try and get 'cashed up'. At this point the world is a big scary place and you need to tread carefully. There is a ton of strategic choice.
After this is the initial land grab. You have found some resources you particularly want so you try and secure these. You will also have met one or two other players by now so there is a bit of a race to get the best spots. Your champion stack of 3 or 4 champions can now defeat medium strength monsters so you don't have it all your own way. You clean out what you can near your base and also explore. No point building troops yet because they are too weak to do much and they will cost you gildar each turn - and money is still very tight. This phase is mainly about developing your champions. Your couple of cities are trying to build city improvements or pioneers. Once again, this is enjoyable because you still have a lot of strategic choice.
Then you get to the 'Champion stack of doom' phase where your champion stack is 'Strong' or 'Deadly' and can pretty much wipe anything other than the occasional 'Epic' monster stack. You now have about 6 champions in your stack and probably 3 or four cities. At this point the challenge has gone and all you need to do is move your stack of doom anywhere you want and wipe the map. This is where you finish off cleaning up the 'Deadly' monster stacks near your starting cities. On a small map you have now nearly won the game but on larger maps you now have to settle in for the grind. You usually now start attacking and defeating other players. You would generally start this phase on about equal footing with the other players but once you have conquered one you will be close to double the score of the nearest computer player. Now strategic choice just comes down to choosing which direction to move your stack of doom and pumping out pioneers to capture more territory. Before this phase you knew the names of your cities and what their role was in your strategy. After this phase the names mean nothing.
The game has moved from interesting strategic choice to boring process-driven rinse and repeat.
Finally, if you keep playing once you have more than double the next players score (that is usually the trigger now for me to start again) you have the added process-driven task of micromanaging your exponentially expanding cities, their build queues, and their caravans. This becomes the final phase for me and I can't play much into it without losing all interest. There are no real choices left to make and it becomes all about micro-management.
So while I really enjoy the way the game starts, I really get bored with it once it hits the middle game. I hope this hasn't been overly negative because I still really enjoy the direction Fallen Enchantress has gone and I can really appreciate the game mechanic choices you guys have made. It is still a good game - just not a great game - because of those two problems.
The challenge is how can the game be kept interesting by shifting the strategic choices to match the phase the game is in.
There has been a lot of discussion about how to fix the Champion stack of doom but for me it has to be about limiting the number of champions that can work together in a stack. Also splitting the XP after combat would be helpful - and perhaps having a third of the XP split between the champions and two thirds split between the troops might help give incentive to make different army stacks.
Starting the game with a small number troops could also help in a number of ways. Perhaps a combination of incentives to keep only a couple of champions in a stack as well as some starting troops is a possibility.
I really liked one of the suggestions in the forum to have troop leadership bonuses that affect just the troops in your stack in meaningful ways but don't affect the champions. This would provide a lot of incentive to treat the champions as generals rather than just Achilles-type heroes.
The city spam is a much more difficult question to find an answer to.
Historically, states and city states had their home-lands and they also had conquered territories that tended to work as vassals. If in Fallen Enchantress you were limited in the number of cities and outposts you could build then this initial pool of cities and resources would become your homeland. There could be some technologies to increase this number over time but basically you would have a small pool of cities you could use to raise armies etc.
When you conquered a city it would simply became a vassal city-state that automatically sent a caravan to your capitol and provided you with its resources. That way these would basically be on auto and you couldn't actually manage them. You couldn't decide what these vassal cities build. And you couldn't use these cities to build troops. You could still move troops in to help defend them.
By doing this you would still keep large areas of wildlands on large maps and you would be focussing on your homeland cities for your development. Newly conquered cities would build their caravan and this would then establish a road to move more troops quickly from the homeland to the frontline. And it would keep the city spam and caravans within your homelands manageable.
By having vassal cities it could also make the Path of the Governor bonuses more meaningful if they could perform certain tasks within vassal cities such as force the recruitment of mercenary troops or affect the build queue. Especially if the Champion stack of doom issue is resolved.
Sorry for making this such a long winded post. Here is a quick summary of the suggestions for those who want to skip all the crap. 
Champion 'stack of doom' solved by making real incentives to limit the number of champions in an army stack.
City spam 'micromanagement hell' solved by having limited number of homeland cities and captured cities become self-governing vassals.
Hope this is helpful and I hope it isn't too negative. As I said, this is a good game but could be made into a great game. 