not want to and want not to?

They mean essentially the same thing but sentence #2 is more clumsy. I would use sentence #2 for emphasis, that is: I wanted you NOT to come here.

Otherwise, I'd go with sentence one. 

Yes.  And for many, they would be identical, but lots of people would choose a different placement for the "Not" depending on what they desire to emphasize.

Also, I would not say the second sentence that way, I would say "I wanted you to not come here." but there are people who would argue that you should not split the infinitive (I do not accept that rule as valid, "to boldly go" is fine and perhaps even preferable, and does not have to be "to go boldly").

For me, whether I would say "I did not want you to come here" or "I wanted you to not come here" depends on which aspect is more important, the desire part (not want) or the coming part (not come).

Imagine never instead of not.  I never want, or to never come?  Big difference to me.

If you're just stating the fact, the first sentence would be universally used. The second would be used in one circumstance I can think of, when the other person specifically disobeyed or disregarded your order or your request. Even in that case more normal would be "I told you not to come here" or "I warned you not to come here."

The difference is between what you wanted and what the other person should or shouldn't do. It's a minimal differerence, but may seem significant bercause of word arrangement.

For the most part, they mean the same thing. There could be a difference in some cases.

"I didn't want you to come here, but now that you're here, I'm happy."

"I wanted you NOT to come here! Go home!"

Your first sentence is the most common way of expressing it. 

BTW, there is an even more complex version.

"Aren't you happy to see me? Did you not want me to come?"

"I didn't not want you to come, but I just didn't think you would. Of course, I'm happy to see you." 

In that case, "I didn't not want you to come" is not the same as "I wanted you to come". It just means the speaker didn't think about it one way or the other.