How hard is it to learn how to program...

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I agree I feel like trying to learn Javascript as a first programming (well, scripting) language would be very discouraging. It seems messy to me.

If I could do it all over again I think I'd learn Java first. You don't have trry about memory, pointers, etc, but you're still working with a language powerful enough to do most things you would need to do. Also if we're talking about bot making, Java is better out of the box than C++ for parsing DOM. In C++ I have to rely on some third party classes for doing that.

I know a lot of people are recommending C# these days as a first programming language but I've barely used it.

Javascript is a full blown programming language with server integration with Node.
How is javascript messy..? Just use standard design practices and it supports OOP like every other language.
You should probably take a look at Eloquent JavaScript: A Modern Introduction to Programming because you severely lack sufficient knowledge of one of the most popular languages in the world.

ALSO DEW JAVA IT'S FUN. SERIOUSLY, LEARN JAVA FIRST! You can make andriods apps, bots, make (shitty) websites etc. I started messing with it around 4 or 5 months ago and now me and a few buddies are developing a game with libgdx.