Given that the time is almost the same, take the two stop.
Reasons:
No luggage or transfer in MDW.
Total time is almost exactly the same.
While at your first stop, you can pick a good seat for the remainder of the trip, maybe even an exit row if you want one.
You get to know the crew if they are nice
Reasons not to:
You might want to carry some food
Using the lav at the stop can be tricky time-wise
If the crew is not nice you may be stuck with them longer
Can't stop at Nuts on Clark