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This is one of my top 5 games of all time, pokemon or otherwise. I've 100%ed it and beaten it multiple times and still had fun. It's extremely easy to make your own self-imposed rules for new types of playthroughs.
I think the biggest issue I have with this game is the lack of map variety. Even though each country's map is unique enough to be interesting, you end up playing on the same maps so many times that it gets stale. It would've been nice (and also fairly easy desu) for each country to have 2-3 maps that it either rotates through or chooses between depending on the scenario.
A more minor gripe I have is that once you get warlords with evolved pokemon it's super easy to steamroll scenarios. Having the game balance itself to your army's strength in a more active way would make the game even more enjoyable.
An even more minor issue I have is that items/facilities are not as important as they should be. It's fairly easy to beat the game without even experimenting with them, and I would like there to be more of an incentive to explore the game's mechanics.
Overall an extremely fun game that I would kill to have a sequel for.