Only in a legal sense are they different cities.
I mean you could legally declare that my legs and upper torso are different people, but it would be silly.
I realise there's history and San Francisco wasn't always joined to San Jose by unbroken urbanity, but arbitrary legal structures should keep up with geography.
But yes, if the San Francisco Bay Area were merged into a single megacity with a unified, powerful municipal government, some of its persistent and increasingly painful issues (imbalance between commercial and residential real estate development, broken public transit system, etc.) might have a better chance of being solved.