In SF, parking and traffic can be a real pain if you own more than 1 vehicle for yourself and expensive. If you need SPACE outside your home to call your own, SF would probably be a bad choice unless you have LOTS of income to afford it. And yeah, SF has LOTS of wild little micro climates. Don't like the overcast? Drive a few blocks.
Daly city is better on space but it doesn't have the prestige of "living in the city". You can get quite a bit more space for yourself though for a lower price.
Pacifica is ONLY nice when the weather is nice, which isn't all too often. When the fog comes in and it does constantly, it can get to be wet and miserable. You'll also notice one common thing in Pacifica other than fog....rust....EVERYWHERE. A few miles away, I can see the THICK fog absolutely pound the coast in Pacific and pour up over the mountains, something out of a sci fi movie.
There are really nice places though most anywhere in the peninsula. I would probably avoid Pacifica though. It's beautiful when the weather is beautiful, but that's not too often. As for SF, REALLY have to consider if $3k/month for rent is worth it or not and that's a low number in my opinion, VERY low.
East bay is FULL of nice places to live for a MUCH more affordable price. But if you work in "The City" aka San Francisco, it's not worth it when you consider the HOURS you'll spend waiting in traffic to cross any of the bridges. I think bridge toll goes up from $4 to $6 in July also. The BART is ok, not too bad, not that great but it can work out if you plan it out. San Francisco is small city, so sometimes I'll take the Bart to the Embarcadero, then walk to the wharf, china town and back to the Bart.
There are great places everywhere though. The only way to really know is to spend a few days, just driving around. However, commuting to SF is TERRIBLE, especially if you're trying to get to the financial district by means of the 101. I have a home at the edge of the city and I avoid driving into SF, it is just a pain and you'll get nickel and dimed to death.
BTW, how old is your child? SF has a really goofy way of enrolling children into school. I am told they use a lottery system. Which basically means your child might be going to a school ACROSS town from you instead of the one next door. If you can, I would look at trying to live in the West Portal district. Somehow, the families there are getting to keep their kids in the schools in West Portal. It's a GORGEOUS part of town.
On the minus side the BART ride from Fremont to SF would take about an hour.
