There are a lot of problems with auto-resolve, and generals are just one of them. At their current pricing (I'm seeing a whopping 30 gold at the start of act 3; that's more than a turn's income for me!) they're just never worth using. You're better off losing the battle and saving the money to reinforce next turn. Maybe after finishing their arcs they get stronger, but right now I'm seeing very marginal improvements (usually around 5%).
