Yes, you can do things like that, but that ends up with you having two different sets of stations that are not easy to get between. The normal pattern is express trains that stop a few times with stoppers that "fill-in" between, but there will be different patterns of stopping to try and optimise for different groups of travelers.

Scheduling/timetabling is a wickedly hard problem, especially in a system like a railway, it's the sort of thing people get Maths and CS PhDs in. The contstraints that you have to solve are complex and interconnected and are part of a bigger network, and you are also trying to please a lot of people with very different (often contradictory) needs.