Where to submit anime idea? If one has come up with an anime manuscript, where or who should you write to if you want to know if the idea is of interest and actually could become something? Or would it be made as a manga first? 

Also, can you like "patent" the manuscript, so that if it actually would be of interest to someone, they don't just change half of the content if they felt like it?
First of all, I doubt they'd look at any scripts not written in Japanese. Second of all, I'm rather doubtful you'd have much success simply pitching an idea to a studio as a person outside the industry. There are, however, many venues to get an idea made into an anime, eventually, but these venues require the person who came up with the idea to produce something.

I'm of course talking about creating some sort of light novel, manga, or comic on your own. These things don't even need to be backed by any sort of publishing company. Japan has thriving communities for posting this sort of original creative works online, such as Pixiv. There are quite a few shows now that started life this way: Wotaku ni Koi wa Muzukashii and Rise of a Shield Hero, to name a couple.

If Japan's TV industry is anything like America's, they are mostly disinterested in ideas. Ideas are a dime a dozen and can be made or broken by their execution. They are much more interested in some sort of proof of concept that the idea will be successful.

As for preventing changes to your idea, you'd have to make sure to put that in any sort of contract you sign to give them permission to use your work. I would guess that would be extremely difficult to pull off unless your work is proven and popular, such that you have enough power by popularity that your idea is good without changes. I feel like worrying about this though is putting the cart before the horse.