After some discussion, some test rides and a lot of talking to locals, I've decided on a Jamis Aurora. Its at the higher end of my budget, but I'm looking at it long term.
The LBS will let me customize components (like for like, pricewise) so I am wondering what I might change from the stock components. At 250 pounds, I am a Clydesdale+ and I will likely use it to carry moderate loads with panniers (Groceries, basic errands around town).
Terrain around here is mostly flat, areas of rolling hills and one really large escarpement. The gearing is likely to be sufficient. Should I upgrade the wheels/rims/spokes/tires?
I would probably buy a B17 saddle at some point...
Specialized.... schwinn..... enough to fill my needs..
I have about 10K + miles on my Aurora now and the wheels are suspect at best. Have your bike shop remove all tension from the wheels and re true them. I had my first Alex wheel go bad after approx 5K miles. Jamis did replace it under warranty though(good on them). I had rim cracking near the nipples and breaking spoke problems. I'm not all that heavy. Maybe 165lbs.
Other than that.... I have only changed out the crank for mountain gearing. Not required if you live in the flats.
The one thing I would suggest is going with the Tubus Logo (rack) for more room for you heels during the pedal stroke.
It's a great bike. You will have many happy miles on the road with it.
I swapped out the saddle, pedals, stem and chainrings and cassette on my '08 Aurora, which I picked up secondhand. I use it as a commuter, townie and light tourer. I changed the chainrings (50/34) and cassette (12-27) to help with the short, steep hills in my otherwise flat neighborhood. All other changes were standard, comfort-driven mods. I added front and rear Topeak racks, but rarely use the front. It's a heavy bike, but once it gets rolling, it's smoooooth.