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Let's get started:
1. First and foremost, I'd like to see a longer and more diverse storyline. I understand that the game isn't focused on the campaign, but the storyline in the fifth installment was, to put it mildly, rather dull.
2. I'd like to see three upgrade options (similar to HOMM5 Tribes of the East), so that each player can choose a specific development path based on their needs, whether it's attack and defense, initiative, or hit points.
3. I also think it's silly for the Necropolis faction to resurrect creatures after a battle using dark energy. I understand that this is a faction ability, but it still feels a bit unfair. :)
4. Finally, my last point: Personally, I think 40 levels of development is a bit too much, because when playing without cheats (as I do), it's almost impossible to reach level 40 and, consequently, develop a special skill. Therefore, it would be better to reduce the number of levels in the game to, say, 20-25, even if it means sacrificing some skills and abilities. :)
I didn't want to go into too much detail; I only wrote down the most important things.