Which university is considered the flagship for the UC system? UCLA or UCB?
There can only be one
The premise is flawed
Both
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Big state with lots of historical funding for higher education.
Cue Queen:
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Sorry, tradition demands there only be one…clearly you are not a traditionalist. 
Try telling that to UT Austin or UF Gainesville. 
Based upon Quora: Berkeley is THE flagship based upon its status as the original campus at the founding of the University.
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Traditions evolve. Tell KNBC there can be only one flagship station. Tell Macy’s Union Square there can be only one flagship store. Tell Michael V. Drake that he must designate one campus - not two, not zero - as a flagship.
Otherwise, it’s all just a fun (?) party game. 
Cal. Clearly.
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I always thought it was Cal but I’ll defer to Californians and alumni.
According to the system they do not have a flagship but most consider it to be Berkeley. Hence it’s Cal ?
Why does it matter tho ?
I dunno, can you tell Air Force 1, they are not the flagship, and Air Force 2 is……no……there is something uniquely discernible about being the flagship.
After all the flagship is the standard bearer, the one that sets the “standard”, the one all others follow…….is that UCB or UCLA?
In this total fantasy party game, since UC designates neither as the flagship, it’s the first campus in the timeline.
Well it looks like 4-0 (and Quora) in favor of UCB.
The UC System is the flagship. UCLA and Cal are generally considered top campuses in the flagship system. If this isn’t satisfying, them call one the California flagship and the other the US flagship. After all there can only be one flagship for each, right?
There are current two VC-25s that provide primary duty, though any Air Force aircraft on which the POTUS is a passenger uses the AF1 call sign.
Those two planes are usually SAM2800 and SM2900 (their tail numbers) any other time they’re in the air, though they can chose another if they want to.
So many aircraft can serve as this “flagship”, and the usual suspects are told they are not “flagships” most of the time.
“Traditional” AF1
AF1 that flew out of Southampton, with its short runway. A C-32/modified 757.
What does “flagship” mean in this context? The best (highest ranked)? The biggest? The oldest? Only on that latter criteria does Berkeley win over UCLA.
But in most other contexts (including the original naval one), age has nothing to do with it.
In this case flagship (would be definition #1) and is always associated with POTUS not a particular airframe, as well it should be. But we are talking about definition #2.
Definition of flagship
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the ship that carries the commander of a fleet or subdivision of a fleet and flies the commander’s flag
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the finest, largest, or most important one of a group of things (such as products, stores, etc.) —often used before another noun
Here is another definition of flagship when referring to a “flagship university.”
“A flagship university tends to be the most known university in its state. It is generally the first public university ever founded and the one that receives the most support from the state government. It’s an institution people tend to search for the most, one with a good doctoral program profile. The majority of flagship universities count with and NCAA Division I athletics and are members of the Association of American Universities. Both groups are very important in the United States, being a part of them is a sign of leadership and prestige.”
I know the OP question is specifically about the UC system. But this question could be asked of other states. For example, UGA or GaTech. UGA is commonly considered the flagship and fits the definition of flagship university as it was the first founded. Based on the first definition of flagship, arguably GaTech could be considered the flagship as it is commonly considered the most prestigious.
As an east coaster with no connection to the UC system, if asked I would consider Berkeley the UC flagship simply based on reputation. No data to back that up! 