Amazing work guys. The new features and changes are just amazing and I trust in your design skills even more now. Some personal comments:
1. Weapon differentiation through abilities - YES. This is probably my favorite change. It adds strategic depth and makes weapon choice actually FEEL weighty. Differentiation through abilities is much better than through statistics.
2. Champion skill progression - This is also a wonderful change. Random choices in FE felt constraining and frustrating, especially if you only got poor choices. Furthermore, it gave you no idea how one choice would impact future choices. This is definitely the way to go.
3. New unit types - also a very welcome feature. Adds much variety.
4. Faction prestige - removing this is the only change I would disagree with. Faction prestige was a very inventive way to softly constrain expansion. By replacing this with more unrest penalties, the game is moving in a more penalizing direction (e.g. Civ 3). The best game design is one that presents the player with two strong choices, not one where a strong choice is balanced with a weak one by just being penalized.
In this case, the choice is between vertical development of cities vs horizontal expansion. The problem in FE was that horizontal expansion was almost always a better choice than vertical development because growing a city gives far fewer returns than settling new cities. Fixing this by penalizing expansion with unrest is the wrong way to go - it turns the player's decision-making into balancing the benefits of expansion with the penalties. Instead, the player should be deciding between the benefits of expansion vs the benefits of development.
This can be fixed by giving larger cities some actually significant bonuses to research and production, or to be able to build better units, or even free units upon leveling up. Or, in the theme of abilities over statistics - how about some powerful "abilities" that are acquired by larger cities? Give the player a reason to build up a city rather than just build a pioneer. Don't just punish the settling of a new city.
Other than that point, I love all the other changes. Separate sliders for production. No more heroes on the map. Getting rid of influence. All of these are excellent changes, and I look forward to supporting your company and buying the expansion!