I'm new to the board but love to give my two cents so...
I definitely think you are on the right path to get a daily driver. I kept my PT for that reason - although to be honest, since I bought the Crossfire, I've driven it to work more often than the PT. But that's only because the snow hasn't really set in yet. Any front wheel drive with some good snowies on it should be fine for commuting in winter. I don't know how the Subarus are these days but back in the 80s/90s they had great gas mileage and you could totally drive them into the ground with nary a problem (I've owned two - a wagon and a Brat).
As for auto vs. manual - my first car was a '62 Chevy II, my first and last automatic. Only stick shifts since then. I much prefer the control I have in a stick plus I love manual transmissions for the very reason you mentioned - the full on engagement of driving. I just really like driving whether it's in the mountains for the day or making a grocery store run. And the more you drive that MT, the more it will become second nature. Not that I've ever nearly put my foot through the damn floorboards looking for the clutch when forced to drive an automatic, lol.
Oledoc2u nailed it for how to drive a stick in heavy traffic. But if that isn't the type of driver you are then you will be miserable. Lol, you think the MT Crossfire is rough in stop and go traffic - try an air-cooled motorcycle on a hot summer day...soooo not good, lol.
Anyways, best of luck with your decisions and may you be happy on the road regardless of what you're driving.