I think many hubs is probably the right answer, but it depends on the goal.
If the goal is to feed people into MIRI, or generally advance some single community organization as far and as quickly as possible, then the benefits of centralization are well known and hard to overstate. Similarly, if the goal is to have a social environment for rationalists, where one's friendships and broader social circles mostly involve other rationalists, then one hub is also clearly the best goal.
However, if the goal is to spread awareness of rationality, raise the sanity waterline generally, grow the movement, or find new ideas and fruitful applications, then many smaller hubs are a vastly better option. All of these things are encouraged by putting rationalists in differing environments, where they contact a wider variety of people, ideas, and problems.
It seems to me that the stated goals of the community are the latter, and so the "right" answer is obvious. We should be encouraging people to find and befriend like-minded people in their local area, and introduce the ideas to their potential rationalists. Have many friends, rationalist and not. Figure out how to talk about rationality's greatest insights quickly and concisely, so you can give people that ah-ha moment and get them hooked. Etc.
To be clear, Berkeley people have a community too, and I don't think we should tell them they have an obligation to move out and evangelize, like early Christian apostles. But I think we should stop encouraging people to move there and if someone is fed up and wants to leave the Bay, they should be bid a happy farewell.
Just wanted to toss the Colorado Front Range (esp. Denver, Boulder, and Colorado Springs) into the hat, since I have a hunch this list might get referenced a lot in future conversations. I don't think we're the best choice for primary hub, but I think we are a very attractive destination for rationalists looking to relocate out of Berkeley and/or for a secondary hub.
Pros:
-We have an existing rationality community, with regular meetups in Denver and Boulder (I host the latter). I know there's local EA meetups as well, though I'm not plugged into that scene.
-There are lots of STEM jobs in the area. We have several National Labs, lots of Aerospace contracting (Ball and Lockheed, Northrup, Boeing, Raytheon), plenty of big-name software companies (Google and Amazon both present, Microsoft in nearby Fort Collins), as well as innumerable smaller and growing ones. Also startup-friendly: Boulder County has the USA's highest VC investment per-capita.
-Outdoor culture means it's easy to stay healthy while enjoying yourself. Biking is big and growing; bike paths and bike-friendly roads are common. Mountains are always in sight and make hiking, skiing, etc. all easy. We have reliable sunshine year round, and winter frequently sees days/weeks warm enough for comfortable outdoor recreation. I think this is all huge for quality of life, even if it was not all included in the considerations.
-Cost of living is very cheap by major metro standards, though not in absolute terms. Median home prices are 450k in Denver, 800k in Boulder, and 350k in Colorado Springs. Everyone complains about the price of housing because it's increased dramatically in the past decade, but salaries still go much farther here than elsewhere. Even Boulder, known locally for high prices, is 40% cheaper than the disaster that is Berkeley.
-Misc: We've got really good craft beer, farmer's markets, a growing foodie scene, and vegan / Gluten-free options are everywhere. Politics are not completely crazy here. The cities are growing so (except in Boulder) development is happening and often welcome; new urbanism is popular, though no one seems to know how to make it happen. Crime is low, schools are good. People are friendly and don't hate each other as much as I've seen elsewhere.
Cons:
-Denver is not a global metropolis. It's the cultural and economic hub of the mountain west, which makes it more significant than you might expect based on population and location. And it has an international airport for easy travel. But some people really want the amenities of a top-20 world city, and Denver isn't.
-You'll want a car. You won't absolutely need one, if you live in Boulder or Denver, but you'll want one, especially for outdoor recreating. Distances are often too large to cover practically on bike. Public transit gets you everywhere you need to go (and lets you take your bike with you) but it's inconvenient. This is true of basically everywhere in the US outside of small areas in the downtowns of a few major cities though.
-Misc: Seafood is not excellent, as we're 1,000 miles away from the nearest coastline. High elevation makes sunburn more likely, and may be mysteriously associated with depression, (though the constant sunshine's got to help on that front). Wildfires make for a week of bad air quality in a typical summer, though hellscapes like Berkeley is used to are rare. Likely other negatives I don't see since I really like it here.
Depends on your preferences:
-Very hot and very cold weather exists here, and the climate is dry. We are a politically moderate state overall, but the most walkable/transit-friendly areas of Denver and Boulder lean hard left.
A minor note: One of the greatest things here quality-of-life wise is the culture, but the culture has been disrupted a bit by recent immigration from other parts of the US ("transplants"). That makes me slightly trepidatious about posting something like this. If you think about moving to Colorado, please do it with the intent to coexist with the local culture, rather than to reform it.
I also think centralization in Berkeley causes damaging PR problems, and that this is a significant point in favor of many hubs. But that's in a comment because it deserves separate attention and may invite passionate response.
A story:
I was rationalist adjacent for a long time, but I never spent much time on LessWrong.com or felt like a member of The Rationalist Community. Partly, I was intimidated by the posters here and had (still have) some pretty core philosophical disagreements. But a lot of it was because every time I came here or to any other rationalist's blog, I would see a bunch of obliquely-referenced personal drama and inside baseball stuff about the community in Berkeley.
Eventually, Scott's SSC Meetup Everywhere post convinced me to check out my nearest group. I met some really cool people, who were a lot more normal and friendly than I'd been led to expect. Now I run a meetup in my local city, and do some outreach. I'm pretty sure that I'm the kind of person who's a really good fit for joining the cause, the kind we want more of. But I didn't know it from the online community.
Rationality is already pretty weird, and rationalists tend to be quirky people. But my experience visiting and reading about Berkeley is that merely living there encourages one to spend freely and frivolously on weirdness. (I mean this of the city generally; not the rationality community there, whom I've never met and know only by reputation.) If you want to raise a kid and live together in a single house with your 5 best friend-and-sexual-partners, it's no business of mine. For all I know, I'll be thanking you in 100 years for discovering the optimal living arrangement. But it's a very Berkeley thing, which leads to very Berkeley problems, which all tend to be viewed pretty negatively by the outside world.
To the extent that rationalists centralize in Berkeley, public forums become largely Berkeley-specific forums, in which weird, Berkeley-specific problems (social drama, weird living arrangements, etc.) are a normal and noteworthy topic of discussion. Even if there's not frontpage posts, it leaks out into the public through comments and offhand mentions in discussions about rationality. And that weirdness and drama leakage can really turn people off from the movement who aren't in Berkeley, even when they're really attracted to rationality as a practice and movement.