I admit Cogmind's approach to resolution is pretty non-standard as far as games go, and it's made a little harder to understand/handle by the fact that the UI cannot be dynamically resized once the game has started. One compromise I was thinking about is enabling the game to restart itself after changing map size, so you can immediately see the effects. @biomatter: You shouldn't have to manually edit the config file--as the options help text explains, you can change map dimensions from the menu but a manual restart is required before they can take effect.
Most every other game allows you to specify an explicit resolution because they use scaling, or can at least show an arbitrary amount of view space, but Cogmind has to both show a multiple of the base font dimension and also offers many font sizes so the player can choose what suits them best (though the largest is chosen by default).
This approach essentially trades ease of use for flexibility. The idea is that it might take a little bit longer to get the view set up exactly as you want it on your system, but once you do it should look pretty good and you never have to fool with it again.
The main issue with allowing the player to specify a resolution is that Cogmind doesn't use scaling at all, and won't change your desktop resolution. Doing this opens the door to allowing your video card to scale the game however it wants to in order to fit your screen, which makes the game look pretty terrible...