1) It's a Tower sim and you are right; there are some airports with multiple ramp towers for ramp traffic but the airport control is done from the tower cab (or from the virtual tower on some new facilities but that's another story :) )
2) Noted, we added into our list to check
3) if they get bigger then it will be even harder to click. We tested a lot for the optimal click spot size. We know it's not the perfect, but please believe me this is one of the best. Please try to zoom in and out on the map for better result.
4) If you select random then the system will choose (or mix) from more than 8 weather patterns
5) Hold short for runway should be fixed. The planes should stop before crossing a runway.
Thank you
Vic