I just came back from Vancouver on a business trip and I can say Vancouver is pretty nice relative to SF haha. Cleaner, less homeless people, safer overall feeling, and less jerks than SF.
What is the price range for your hotel? That would be a good starting point. If you're here only 4 days, staying in SF would be nice. The Hyatt on Embarcadero is nice, and while I haven't stayed in the W in SF, they are generally good to go.
If you don't intend to leave SF itself, just take a cab from SFO to your hotel. Parking in SF can be expensive and sometimes scarce, so you can always just take a cab. Either of those two hotel choices are good for walking to certain attractions.
The Mission district has some nice up and coming eateries, but it can be somewhat sketchy at night. It isn't terrible, but don't say I didn't warn you. I don't mind going there by myself, but not somewhere I'd really take my kids.
A few family friendly yet good places to eat:
Tadich Grill (financial district/downtown)
Thang Long (vietnamese style crab and garlic noodles, outskirts of sunset)
Cha Cha Cha (Cuban food in Mission)
Bobo's (Boboquivari's, a steak place on Lombard near Van Ness -- get the bone-in filet if they have it)
If you Bart across to Berkeley, off the Downtown Berkeley exit is Angeline's Louisiana cajun restaurant, awesome food.
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