I think either would be fine. If you happen to live in hub city, you have a better chance of flying non-stop to your destination. Non-stop is always my first choice, less to go wrong, takes less time to get to where you are going and less opportunity for lost luggage if not switching airplanes. Depending upon where you fly, it is also better to stick with one airline if you can so you can accumulate enough frequent flyer points to be worth something. Having points spread around with different airlines usually means you never accumulate enough for any upgrades.
I believe all of those commuter flights are now jet aircraft. In the past some of the shorter flights used propeller aircraft which were typically noisy and flown by the least experienced pilots. Something to avoid if possible. Good to check the flight 'details' about the type of aircraft when booking your reservation. If you happen to live near a small airport, you will typically take a commuter plane to connect through one of their other larger airports. At large airports, commuter planes generally have their own terminal and you have to walk a long way to get your connecting flight.