I'll chime in from the other end of the spectrum. I use a MacBook Pro and love using the built-in trackpad when I'm mobile. Since I like using the built-in trackpad when I'm undocked, I thought I would like using the Magic Trackpad when my MBP is docked on a stand...but it turns out I don't enjoy it quite as much as I thought I would.
With the trackpad on my desk, I'm finding it's somewhat uncomfortable to use after a period of time. Mainly because I have to rotate my hand/wrist to be more horizontal when using it. Whereas with a mouse, it's a little more ergonomic since I can have my wrist in its natural, slightly rotated position.
I also use a triple monitor setup when docked, so to move from one end to the other, I have to swipe the trackpad several times. This means my arm mostly stays still, but have to bend my wrist a few times to move the cursor. With a mouse, I can just slide my hand and forearm in one motion.
Having said all that, I do still have it on my desk and use it for the gestures, but primarily use my Magic Mouse for everything else. I'd say the trackpad works for some people, and not for others based on their desk setup and work flow. Personal experiences can also vary. Perhaps you could borrow one from a friend/co-worker to try out, or purchase somewhere that has a good return policy in case you end up not liking it.
