At times the game will give a message saying that the map space is too small and battle needs to be resolved automatically.
Since certain battles (eg fortress) are never resolved automatically I know that it is possible to give all battles the possibility to be resolved manually.
For those who would point out that fortresses are static, there are other battles (eg stellars) that are also never auto-resolved.
I wouldn't mind if the auto-resolve was even slightly competent but when an auto-resolve ends in a win where I lose 90% of my units in a battle where I can win with zero damage to a single unit if fought manually, I have a big problem with it.
Unfortunately with the game in it's current form it is absolutely unavoidable because terrain features mean that sometimes when you siege a city you end up with a battle that must be auto-resolved.
Please if there is no plan to make all combat optionally manual, at least let the player know that a battle will not have that option before they commit to it.