Ok, so in the end I took the free swap. I think I would have been in trouble if I hadn't, as I think the LBS really went out of their way to arrange the free swap under warranty.
Observations:
* Pads now have a few more millimetres of clearance, which is a *huge* benefit in muddy conditions
* Much sharper braking, like going from nothing to good stopping in a short range of lever movement
* On the converse, it takes more hand pressure to stop. Logical, but something I didn't think of.
* Slightly more fork shudder. Previously I could induce shudder by braking while rolling at like 1kph. Now I get it up to say 3-4 kph. Definitely not an issue under normal circumstances, but something I'll keep an eye on.
So it's worked out well so far. The feel of braking is much better, none of that long "whooshy" sound before the bike actually starts really slowing down. And I almost never "bottom out" the levers.
Of course, now I'm wondering why I don't just get disks
This weekend went for a ride through the most horrible ever mud of death, like big chunks of clay and sand. My friend with disks was ok, but for me the mud started to cake up in huge wodges around the cantis and eventually start to prevent the wheels turning. It was pretty bizzarre. I was amazed how well the bike performed under all that mud though - changing gears was still fine, despite centimetres of mud in the front dereailleur, a solid film of mud over the chain etc.
Re: darrenmc's post, I'd have to assume that the brakes I got originally weren't "mini-vs". From what I heard from the LBS, the distributor was careless with what brakes they shipped, then realised their error, and corrected it. They wouldn't have done this if these brakes were designed for the bike. And also, I wouldn't have this big difference in handling and setup (ie, pad clearance).
I guess if I'd known about the "mini-v" option I would have asked them about it. But I think I'll be ok with the cantis. Brakes aren't something I really want to spend money on.
Steve