You are right. I am looking at the long run.
If you are looking at the long term, you need to increase your scope and forecast your family needs for the future. It sounds like you have no kids at the moment, so if you do raise a family, you definitely need to be closer, both in terms of the time spent with the family and the constant immediate things kids/families need. Does this have a good school district, etc.. Remember time is money, thus your flushing money down the drain sitting in traffic.
I just moved back to the Bay Area a little over a month ago, spent the last 9 years in the Pismo Beach area. In Pismo, we had a larger home, the wife worked 5 minutes away, kids schools were down the block, everything was close by. Both of us went to the gym 5 days a week (during the work week) and we were still able to cook dinner at home and have plenty of time with the family during the weekdays.
When we moved back to the bay, we still wanted the larger home, but we couldn't afford some of the places in/around the area (Sunnyvale, Cupertino) where my wife got transferred to. So we went to Fremont where the rents were cheaper, but the commute was longer. We figured we're from the Bay, we've done bumper to bumper traffic before, it's not a big deal.
Needless to say, my wife HATES the commute. Yes, we have a bigger house to go home to, but she wastes a lot of time stuck in traffic. She spends an hour or more getting home each day. So we can't do what we were doing before because our whole schedule is off.
These are things you need to consider too. Remember, time is money.