You say 30,000 but your notes suggest about 100 miles per commute trip. Assuming you'll not commute 2 weeks of the 52 work weeks, I come up with 25,000 miles. Any more and the numbers below only get more in favor of 2nd commuter car....
Damn, jwest...are you going to make me pull out a calculator?

Okay...
Let's go with 19,000 miles a year commuting (4 days a week, 48 weeks a year, 100 miles a day), at most.
Outside of work I have been putting on over 17,000 a year, which already subtracts out my old short commute.
So, I'd be at 36,000/year with the new setup.
Actual costs at the pump are averaging $20/trip with Premium costing about $3.80 now. That seems more than it should cost based on the average MPG I see...but I guess it takes into account more details than I care to go into. In the end, if I don't do much other than commute for 3 days, and it cost me $60 to top off the tank at the end of 3 days...I'm calling it $20/day.
Miles...ugh, well that depends which way Waze tells me to go each day. Can be as low as 36 miles per trip (with some real slow bumper to bumper sections), a highway route closer to 50 miles, or up to 60 miles if I'm routed around accidents and in those cases I'm in the car for a while anyway. Again...doing rough math I was averaging around 100/day. Ideally, it should be less but my gas is still around $20.
You are right on the fuel economy. I did the math initially a few times and couldn't figure out why I was spending $20 a day. It doesn't add up based on what I know I can get on a highway trip. So I guess it's the stop-n-go slow traffic.
Hard to not consider a new tdi:
$1000* Fuel Reward Card on new 2013 and 2014 VW TDI models
$1,000* Fuel Reward Card plus 0.9% APR** for 60 months
...
That's interesting. I was finding used ones, CPO, that I liked for around $20K. The new ones (with sunroof) are going for $26.5. So, the fuel card gets you down a $1000...however, I found they don't always mix incentives so it is worth poking around. You may only get price incentives OR the fuel card incentive. Not both.
...
I ended up leasing a Honda Accord Sport 6-speed manual ($22,005) - one of C&D's 10 best. It does not have a lot of creature comforts, but does have dual exhaust, 10-way power seat, quick steering, and 18" wheels etc. I added Nokian z-line tires and Weathertech everywhere. It is a lot of fun to drive (suspension, gearbox, steering) - miss the torque, and is supremely comfortable (I'm 6'3" and 210lb). Driving very energetically I still get between 28 -32mpg. Plus the Accord has more room in the front and rear seats - lots more, and I can fold down the rear seat (now) and put in my bikesurfboard; which I could not do with the Sport. ...
This one was not even on my radar. If you can fold down seats and fit in a surf board, that is worth looking into. I wouldn't be getting the 40+ mpg of the TDI, but, diesel is $4.20 a gallon and I'm guessing you can put regular in the Accord. I don't know what they cost yet but it could be worth looking at.
I appreciate the thoughts on this and am no closer to a decision.

I do want to test drive the A3 which I haven't seen in person yet. I hear it is a little smaller.
I'm having a tough time accepting a car as just a commuter and throwing away all the utility aspect, which is why I was just looking at 5 doors. It seems that a couple days a week I am throwing some sporting equipment in the back of my LR3 that I still want to be able to do on the JSW. When I tried out this setup on the JSW I found out that the seats are a royal pain in the ass to fold down! You need tools to get the head rests out of the rear seat backs in order to get them to fold down. There is a small door that opens up which would only fit a set of skis (I don't ski) so that has no use for me unless I'm using it to haul a few 2x4s around for some reason. LOL
Anyway, still leaning towards the JSW for all the reasons you pointed.
Will take a look at the A3 and the Prius again...just for yucks, and maybe that Accord.