Yeah, there's always a trade-off when it comes to puncture protection. My current 3 commuters have:

1) Bontrager Race-Lite Hard Case
2) Continental City Ride
3) Schwalbe Marathon Plus

and so far 1) and 3) have never once had a flat; however the Continentals are so much nicer to ride on than the others (but have had 4 flats in the last 4 months). Hard to describe but the Marathons feel like riding on solid rubber with no air, and the Bontragers feel really sketchy on gravel, mud etc. The City Rides are just right.

It's a tough call. I plan on swapping the Contis out for the dark season because I really don't want to replace tubes in the dark. They'll be back in the spring!