Re: Getting a Nevada LLC as a Californian
The annual fee you'd perhaps be paying California isn't a penalty, it's a so-called franchise tax, a charge for the privilege of doing business in California.
In general. Corporations and LLCs must register, file returns, and pay franchise taxes in (1) the state where they are formed, and (2) every state in which they transact business.
So, if you live in California, form a Nevada LLC, and the LLC then owns and manages a rental property in New York, the LLC will probably have to register. file and pay franchise taxes in Nevada and New York.
If it simply owned real estate in New York but didn't participate in its management (i.e., didn't interview tenants, arrange for repairs, etc.) then maybe it wouldn't have to pay New York franchise taxes, but this is a question of New York law and I can't offer an opinion.
The LLC would not be liable for California taxes purely on the basis that it had a member who was a resident of California. However, it sounds as though you would be the managing member and would be performing some management functions for the LLC from your residence in California (or from an office or whatever). Even such a minimal level of participation as keeping the LLC's books in California, using a California address for correspondence about its affairs, etc. could constitute doing business in the state and oblige the LLC to resgister here as a foreign LLC and pay the California franchise tax.
Why would anyone living in California form a Nevada LLC to pursue a business in New York? It won't save taxes, it will increase them, by adding an unnecessary obligation to report and pay in a second (or third) jurisdiction. I've formed two Nevada corporations myself, but for the express purpose of owning and running businesses located in Nevada.