There are two routes you can take when penning fiction in an urban environment. You can either fictionalize a real city, or you can just make up your own out of whole cloth. They both have their own merits. Using a real city gives the reader a sense of familiarity, but you also have people that will not appreciate your diverging from reality or just plain getting stuff wrong (and you will). On the other hand, a fictional city gives you a lot more flexibility, but also can serve to diminish the connection to the real world.
From my frame of reference, it's the DC/Marvel thing. At DC, Superman is in Metropolis and Batman is in Gotham City, and these two burgs can co-exist despite both being analogous to New York. Hey, they can even somehow co-exist WITH New York, which is where even I have trouble rationalizing the matter. Meanwhile, over at Marvel, the main stomping ground for their superheroes was established fairly early as being New York City. Of course, things like Avengers Mansion don't exist in the authentic Big Apple (sadly). In practice, Marvel's New York is only a smidgen more connected to reality than the homes of the Daily Planet and stately Wayne Manor.
I made a decision in the process of defining my personal superhero universe (the "Owariverse", if you will) that I was unconcerned with having any meaningful connection to reality. I wanted a world where I had the latitude to do what I wanted, without having to concern myself with pesky "facts" if they didn't serve my storytelling purpose. I mean, you've seen the sort of characters that I'm using. So I decided that a fictional city was the way to go for me.
I've been using the name "Major City" so long and with such a straight face that I think I have ALMOST been successful in disguising the fact that it began life as a joke. Think about it - the terminology "a major city" has been used forever and a day when the creators want to be vague and generic. I just converted that generic label into a proper name and arrived at Major City. Be thankful I didn't go for "Big City"; Lord knows I am.
As time has passed, I've tried to ground Major City in its own (admittedly far-fetched) version of reality. I even dreamt up a justification for the name by concocting the Major family and positing that the city had been founded by their ancestor Calvin Major. I've filled in the spaces around Captain Satellite and Shelly Ericson by establishing such diverse elements as MTI, Lightning Cars, The Major City Courier, the Mando Building (one of my all-time favorite obscure in-jokes), Mayor Rudy Boemer, and the DeKalb Television Network. Oh wait, I haven't actually established the latter two just yet. Don't worry; we'll get to it.
Obviously, in my world, Major City takes the place of New York. But what about the rest of the country? While I had made the decision that the rest of the world was sufficiently "exotic" for my goals (and I'd probably louse up trying to alter such locales anyway), the rest of the United States was still in play. I kind of wanted at least one other fictional city to serve as contrast to Major City. And if Major City was Fake!New York, the logical choice was to create a Fake!Los Angeles.
My first instinct in creating a California city was to make it a west coast Major City, and give it a Spanish version of the name. This led me to Ciudad Importante via Babelfish, and...wow, yeah, I couldn't do it. I tried other options that meant approximately the same thing like Ciudad Grande, but there was just something missing. I wanted a name that rolled off the tongue easily whether you were a Spanish speaker or not, and the word "ciudad" seemed a mite too difficult for a pseudo-comic book name.
I abandoned the search for a western Major City and turned instead to deconstructing the name "Los Angeles". You know, when you think about it, it's kind of strange for a city to be named "The Angels". However, due to the shortening of its original lengthy name, Los Angeles now has a name that seems unlikely when translated. I could work with this.
After a lot of thought, and more than a few attempts, I settled on "El Oceano" as the name of my L.A. counterpart. In Spanish, El Océano obviously means "The Ocean". And really, is that any more absurd than a city named "The Angels"? Plus, it gave me the opportunity for a fun musical reference when I announced in a "Twitter exclusive" that El Oceano had been founded by Spaniards Roberto Planta & Jaime Página. Now really, how did I come up with that?
I'm still in the process of figuring out how I want my world to operate. Are the other cities "replaced", or are Major City and El Oceano the only stand-ins? It seems strange to me that New York might not exist, but (for example) Baltimore would. I don't know how I'll handle it. But it's fun to bat these things around, especially when they open up even more story possibilities for consideration.