Thanks for this thread Krom. Here are my thoughts and I have also included some new problems at the bottom which I think should be fixed.
1. Complicated Game Mechanics: This is KAM. This is not a problem. I love how intertwined and complex the town system is. A solution to problem number 12 (Not enough transparency) will make things easier for newcomers.
2. MP Slow game pace at start: NOT a problem. The slow pace in the beginning allows a person to plan his town especially on a map that you have never played before. I use that time to decide where will I build my farms etc. To me, the entire time is being used... and it is relaxing. I don't want KAM to become Starcraft.
3. MP games start by the template: NOT a problem. I use templates on some maps and I don't get bored of them. I'm becoming notorious in the community these days for playing Location 6 on "Frozen Waters" with a template town. I've been playing that same location since 2013 and I am not even beginning to get bored. Some people like templates... some people don't. KAM doesn't force anyone to choose. Furthermore, I've noticed that good maps have remarkably different playstyles for different locations.. and each time I play a new location it seems like an entirely different game to me. It keeps it so fresh.
4. Long time before PvP: This is not a problem for me but I understand this can be a big problem for many people. But honestly, I think thats what KAM is. The satisfaction that I get after building my town for 60 minutes and then going to battle is unmatched by any other game. Thats why I play KAM.
5. Unresponsive army: .. Never noticed it. However, I am really sick of my troops going out of formation when moving large distances. This is REALLY A BIG problem and needs fixing.
6. Army control during fights: I am also sick of this problem. It unrealistic and 1 small mistake can have your entire army of knights butchered by few pikemen. I think this should be changed.
7. Towers and Turtling... not a problem.
8. Leavers, laggers and newbies in MP: Yes its a problem but since we are not talking about solutions here so I will keep the ideas in my head for now.
9. Abrupt game end. Yes I think this is a problem. It can make for a very frustrating game if few knights or even militia of enemy goes into your town and kills all your farmers and serfs and you can't stop it. Some way for the serfs to fight back can really help here.
10. Winning screens: Yes I think thats important. Right now, even the statistics screen works really good for me
11. MP involvement: Yes its a problem. But I think it will remain unless a system for registering players or clans officially is made which I think is not really the top priority right now. There are more important things.
12. Transparency: Read 1. This is important to fix and will make the learning curve easy for newcomers. Should be really high priority and it is very simple to implement I would assume.
13. Maps too small/Towns too big ... not an issue for me. My only issue is moving armies over long distance in correct formation.
14. Troops hunger plays no role. Not a problem... as it is just feeding your town while producing enough army is hard enough and is a challenge. For rather low skill games (where they have 90-120 PT) they have enough time to produce enough food and towers for a long camping game. In camping games they have to feed soldiers. I think it is just a playstyle thing - I don't think it is a problem with the game.
NEW PROBLEMS IN MY OPINION:
15. Not being able to get rid of or retrain citizens. This is really a pain for me... in games I have 2-3 fishermen and many miners and laborers which I cannot get rid of. They eat my food. There should be an option to retrain them into serfs or just send them out somehow.
16. The food producer gets hungry and cannot eat food in inn: .. I have had games where I have lets say 1 butcher... his shop is FULL of pigs but he is hungry. There is no food in the inn and he is the only food producer. Why cant he just make a sausage and eat it in his shop????? If he stops producing food my entire town goes hungry. This can even happen when I have 2 butchers and one goes hungry. If he doesn't find food in the inn (because other people eat it), he refuses to work and my food production becomes slow by half!
17. Cannot build on trees: Can be really painful. I should be able to give the order to build even on trees and the laborer should go and remove the tree. Why? Because this way I can plan my town better and the cost is that I lose that tree. There are games where 1 tree can really mess up your entire positioning of building. And the only way to get rid of it is to use the vineyard on it (thanks for teaching me Ben).
I have many solutions in my mind for many of the problems discussed in this topic. But I will stick to the topic for now. Later when you ask for solutions I will be happy to contribute

.
Here is an updated list. The problems got a few marks:
- means problem is not a big deal.
+ means problem is a big deal
Again we are looking for problems and their importance/non-importance. Solutions will be discussed later!
1. Complicated gameplay mechanics --
Despite the genre the game is still quite complicated to a newcomer, compared to other RTS games. Basic town needs a lot of houses/units/roads/actions just to become self-sustainable.
2. MP slow game pace at the start +-+
The game might me a bit too slow for today, especially at the start. Later on amount of decisions raises and the pace is nearly good.
3. MP games start by the template +++
Players build their towns by templates, always repeating the same formula until 20-30min mark.
4. Peacetime in MP ++
It takes 60 min before PvP action can begin. There is no PvP interaction until PT ends, which makes the game very repetitive.
5. Unresponsive army --+
Controlling army has inherent lag of ~1sec because of tiled unit navigation. Big armies have collision problems, part of the gameplay with armies is focused on keeping the army positioned right when moving and guarding.
6. Army control during fights -+-
Player loses control over groups when they engage in combat. This limits player decision making during engages. Players often try to split troops before fights to try to maintain the control.
7. Towers and turtling in MP
This problem seems to be dealt with, as players realize that towers can be destroyed with archers and/or sneaked by.
8. Leavers laggers and newbies in MP +-
MP games seem to be plagued with inexperienced players who lag a lot and leave them game spoiling everyone’s fun.
9. Abrupt game end in MP +++
Letting enemy into the base means certain defeat. Players can rarely fight back. As soon as player’s defence is breached he is likely to lose and just quits the match.
10. Abrupt game end +
The game has no winning screens and graphics.
11. Low player involvement in MP
Despite being quite popular, MP game lacks support for long-term player involvement: persistent nicknames, reputation, competition, clans.
12. Not enough transparency in core gameplay actions (Duplicate 1)
Quote “Let a mill, for example, display what number of wheat it can process per X time period. Let the bakery do the same, and let the farms show how much they've produced in the past X time period.
Make it WAY easier to see if you need more mills, bakeries, gold smelters or coal mines.”
13. Maps are too small for MP / Towns are too big
Towns take much too many space on the maps. Even XXL map gets quickly occupied by 8 players towns. Yet maps size seems to be okay for army navigation (walking takes long enough time). On a sidenote - XXL maps take too much time and effort to create.
14. Troops hunger plays no role (Caused by 4, 9)
Mechanic does not have a chance to work - troops almost never get enough time to become hungry.
Please post about which problems are important and which are not. Maybe there are some big ones we have missed.