What one has to remember is that Warhammer is mostly a melee combat game which has some gunpower units which are ment to support you melee units. Whereas Empire Total focuses mainly on gunpower and melee combat is used to support your gunpowder units. If you used the Empire Total War engin would you still be able to build a game with factions that don't use gunpower like the Bretonnians or the High Elves, that are effective, fun to play, and true to the warhammer universe? For example as far as I know in Empire cavalry units are light cavalry and are used for harrasing enemies units and forcing them to change formations and such. There is no heavy armoured cavalry like knights of the medieval ages which just full on charged the enemy to utterly break them and run them down. If you used the Empire engine would you still beable to create Bretonnians, or Dragon Princes, or Empire Knights?
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