I've put 1000s of miles on Gatorskins, they are a very puncture resistant tire that still ride nice. They are not as plush as other tires, but they are designed to handle rough conditions without punctures, which they do nicely.
You can still get the older design pretty cheap: http://www.probikekit.com/display.php?code=Y1320
These are the new ones: http://www.probikekit.com/display.php?code=Y0097
You can always to the 25mm wide version and lower the pressure a little bit for a plusher ride.
I like the GP4 Season too: http://www.probikekit.com/display.php?code=Y1094
The GP4 Season ride softer than the Gatorskins but are still pretty good at avoiding flats. The GP4 Seasons are better in really cold (like below freezing) than the Gatorskins. I find the Gatorskins get greasy when super cold, the GP4 Seasons do not.
You don't need sipping or treads on road bike tires, they can not hydroplane (their surface area to psi is not large enough like car tires). The treads are for looks.
Shoes are up to you. I like MTB shoes for the simple reason you can walk without skidding on the cleat easier. Both are comfy when they fit, I've done over a 200 mile one day ride in road shoes and plenty of 100 mile rides in MTB shoes no issues.