withm, I have a similar dilemma regarding commuting and my current bicycle. I've got a very lovely Orbea that I hold very dearly, but she isn't designed for commuting by any stretch of the imagination. One of these days I'd love to find a nice second bike - something like a used touring bike - but in the meantime here's what I do:

Carrying stuff:
No braze-ons to have racks installed, and the fork/rear chainstay are carbon. I've heard suggestions that you shouldn't put racks on carbon anyway. I carry everything on my back in a pretty nice cycling backpack made by Deuter. Downside - hot sweaty back and increased saddle weight. Upside - increased core strength, and my sitbones are probably getting tough enough that I could easily go 80+ miles right now, even though I'm only logging 50-60 miles a week. Now when I ride without my backpack I fly down the road.

Tires:
I'm still using the 700x23 racy tires. As long as I keep the tires properly inflated and choose my path carefully in the debris of the bike lane, I haven't been having many flats. It's true that the bomb-proof bigger tires would probably be comfier to commute on, but they're higher rolling resistance and more energy spent just to move the wheels round and round. You won't necessarily get better traction by going to bigger tires with more tread, if anything you could get less traction.

Security:
At the office we have a fairly secure bike lock that is right in front of the security desk. I've been negotiating with our building maintenance people to get some enclosed bike lockers installed and I think it's going to happen. At my school there is a huge bike theft problem, fortunately there are some city-operated bike lockers and I was able to reserve one of these for $10/month. I simply don't run errands on my bike when I commute, I try to plan my errands for car days or the weekend.

Fenders:
Fenders are a must for commuting here in Portland. SKS makes these Race Blade clip-on fenders for racy bikes that don't have clearance under the brakes for normal fenders. They are a little shifty but they do work pretty well, they don't block all water but you won't show up to work looking like you just crapped your pants on your morning commute.

Lights:
Basic lighting installed on the bike, and additional lights attached to my helmet and backpack.

Anyway, I admit that my situation is far from ideal. Someday I will probably get a dedicated commuter bike, but I want to point out that it can be done. And hey, so what if I drive my "fancy sportscar bike" every day, instead of keeping her polished with a diaper and stored in the garage?