IMHO, there are problems with the idea that different wheelsets are an easy fix.
First of all, I don't think the wheelset really affects your commute time (unless you are commuting 100+ km a day). I've tried slicks on hardtail MTB and it didn't knock more than a few minutes (if that) off of an hour commute. How the bike frame geometry, weight and setup affects your pedalling efficiency is FAR more important, I would say. (ie Its not about the wheels or tires - its about the bike).
Second, it really only makes sense to have a swappable front commuter wheel. The rear wheel requires you to either switch your one freewheel cluster over or to buy a second cluster.
Switching a freewheel cluster is somewhat tedious (I'm lazy), but you may not think so. If you have 2 clusters, you will probably find at some point you will get incompatible wear between your 2 clusters and the chain (depending on how much you ride each cluster). You may be lucky and only have to replace the chain and one cluster, but it is likely you will have to throw away the chain, and the 2 clusters prematurely. For that amount of money over the long term, it is probably better to buy a bike that you can both commute on and do some types of trail riding on and then leave the pig iron for gnarlier types of riding. The amount of time you spend switching wheelsets probably will probably negate the time savings from a better-rolling setup.
This is a good point. I'm drawn to a 29er hardtail as my one bike for several reasons. One of them being I'm pretty sure it would be quicker than a 26er on the road (given similar gear-inches.) The Paradox seems like a low maintenance, jack of all trades that can be built fairly light but strong, and with good geometry for teh trails. Road/commuting would be a small part of its use though. It would be mainly for BC xc/trail riding.
So maybe the second wheelset thing isn't worth it.