I agree that 45 minutes for 12-13 miles when loaded for commuting is not bad for a lot of people. A bike even if loaded with only a change of clothes, lunch, and a small toolkit is going to feel more 'tank like' than the same bike unloaded. That rack is not usable with panniers, but a light pack securely strapped to that rack should be just fine. The center of gravity is going to depend more on your body weight and position than moving a light load a little bit lower. Going to clipless pedals really won't change that much overall. If you're never using the inner chainring, and spinning too fast in your highest gear, you might want to increase the size of your chainrings by 10 or 20 percent (each). Switching to a rigid fork may improve things. If your suspension is bouncing as you pedal, that energy could go toward movement. You can always go to lighter tires or (for more $$) wheels. Durability is often more of a priority than speed for a commuter bike.