I agree with Kacee. I always try to do the online check-in. If I have been pre-upgraded and get to really choose my room, I complete the process. If I don't see the pre-upgrade and think that I might do better without completing the process, I just let it go. The message when you do the check-in is that they will still try to upgrade you when your arrive in the hotel but some hotels are really cheap (recently there was an example on the Hilton threads about one of those hotels in Boston) where they tell you: "Well you chose that room, so you stay in that room".
For the uncertainty about being able to get to the hotel if the weather is really bad, I consider that I already have a problem with that since all the hotels have a cancellation time. The Hilton I'm going today used to have a 48 hours cancellation, it just switched to a 72 hours. I think if the weather is really bad, the hotel can make a judgment about that and not penalize you for already checking-in. Not only that, but if you end up having to pay for the first night and you are traveling for work, work better pay for it. My employer does that. As it should.