I second what Lance has said, and have a few things to add. The 53/39 is a pretty standard crank. Things are moving into compact cranksets (50/34) and that is what I have. That gives you more in the climbing end. 12-25 is also pretty standard. They make an 11-28 now, which would give you better leverage for uphills, and more speed in your 53-11 (vs. 53-12). As far as being good for climbs, your legs will tell you.
The Bontrager wheels are not stock for Giant. They're owned by Trek, so you'll find them on Trek, Gary Fisher, Litespeed (I think) and Klein. They're pretty expensive too, about $320 (MSRP) each. Aero wheels are heavy because of the shape, but you're supposed to gain some better aerodynamics from them. The Bontrager are about 1775g for the set. To put that into perspective, my Mavic wheels on my new Scott are 1550g for the set. About the same price but non-aero. The Dura-Ace wheels that came on it were probably about the same price, but non-aero.
The tires are OK, but I've never been a fan. The GP 4000s that I get are around $60 per tire, but worth it IMO.
As Lance said, SADDLE. That is the most important feature on your bike, and one of the few things you NEED to buy retail. The reason is because many have trial periods (make sure you check on this, do not get a saddle without a trial period). You need to try new saddles until you come across the "right" one. Keep in min, however, that it needs to be firm and needs to support your sit-bones. If the boys or the pee-pee go numb, it's not the right saddle (make sure it's level and only make minor adjustments). Your sit-bones will probably be sore the first few weeks, that's normal. Expect to pay anywhere from $100 - $200 for a good saddle.
Get padded shorts. The road-bike lycra kind. You'll look like a dork.
Finally, just ride.