make them work only with capships, small ships have to take the normal station dock bays.

-1 But there should be something funny as a penalty for doing so. Maybe a warning or a docking fee for using the wrong dock.

Of course any effort in this direction could cause issues with the docking at M7.

-1. Why is this even a concern? Is it because they're easier to dock in? I don't really mind that, since only capitals have them.

I agree, it's important for an issue to be a legitimate concern before making a change in game.