A crank-drive bike just isn't as relaxing as a hub-motor on a long commute because you have to be in the right gear all the time. When I was commuting 30 miles a day, I tried both. I found that the hub motor was a lot better, especially in the winter when you have cold hands. All that gear-changing on the CD becomes very tedious, especially as they go with a bit of a bang each time.
Another obvious drawback of CD, is the much more frequent replacement of chains, cassettes and derailleurs. When you get a problem with any of them, you have to push the bike (sometimes carry) or order a taxi. With a hub-motor, you can still pedal or throttle home with no chain.
With a hub-motored bike fitted with Marathon Plus tyres and hydraulic disc brakes, you could probably do two years with nothing more than oiling the chain and the odd bike cleaning. My bike has done 4000 miles since I built it, and hasn't needed any more than that apart from one gear-cable broke which was used a used one that I bought from Ebay when I built the bike.
There's quite a few of us that have done these sort of commutes on hub-motored bikes, but I haven't really heard of anybody doing them with CD bikes. I think somebody mentioned using a BBS02. Maybe somebody that does can chip in with his/her experience.