A couple things to consider:
--Infinity's revised AK itinerary does not include Skagway; Mercury's does. I don't know anything about Sitka, which is now on Infinity's itinerary instead, but we enjoyed Skagway most of all when we sailed Infinity to AK last year -- it's the gateway to the Yukon Gold Rush route; many take the train, we rented a car and drove into the Yukon. I would have hated to miss that.
--Because of the Vancouver departure, Infinity cruises the Inside Passage in both directions. Mercury is listed as only cruising the IP on the way back. If it's really in the more open seas on the way up, things may be a bit rougher, and less scenic. We found the IP absolutely drop-dead gorgeous in both directions, and the seas quite calm (though we certainly don't mind rough seas since none of us are seasickness-prone).
Just a couple things I'd consider. As for the ships ... we've been on both now and they're both quite spectacular, although I am developing an addiction for the C-class (century, mercury, galaxy) thalassotherapy pools ... the free one on Infinity was no comparison ... but that wouldn't be a dealbreaker!
Mercury 4/04, Infinity 8/03, Century 3/03 & 9/02