Human beings derive joy from doing good. Studies on happiness find that this is one of the bigger correlates of happiness. If you're at all normal, there's probably a lot of room for you to do more good and be happier.

As for intrinsic motivation and System I... it's difficult, updating your System I isn't as straightforward as updating your System 2 (aka using evidence to update your beliefs). One day I plan on writing a post about this...

However, there are some things I'd like to note:

I guess in part it's because I expect genuinely trying to improve things (rather than making a token effort) to be a rather difficult and thankless task.

I don't think it's that difficult or thankless (although I'm definitely in the minority here and I don't know anyone as optimistic on this front as I am, so take that for what you will). For example, take this very website/community. There's tons of relatively simple and straightforward improvements that could be made that I think would have a relatively high impact. Like making the website easier to use and including new features. For example, adding a section that makes it easy for LWers to brainstorm and collaborate on projects. That's a high level action that I could see trickling down and having a big impact. And if you're talking "genuinely" as in making fundamental changes to the way things work... I've got some thoughts here.

Also, as far as I can tell, my psychological makeup is such that feeling, thinking or being told that I'm "obligated" to do something actually decreases my motivation. So the idea that "I'm supposed do that because it's the ethical thing to do" doesn't work for me either.

Me too :/. I think that it's easy to give this spite too much weight as you make decisions. To some extent, I think it's ok to "let the spite be". Trying to exert complete control over these sorts of emotions is too stressful. Whatever marginal gains you make in making your emotions "more accurate", it's probably outweighed by the stress it causes. Finding the right balance is difficult though.

I do like the idea of making the world a better place as long as I can do that while doing something that inspires me or that I feel good about doing. Part of the reason, I think, is that I don't see myself being able to do something I really don't enjoy for long enough that it produces meaningful results. So in order for it work, it pretty much has to be something I actually like doing.

I think that you'd be more motivated if a) you thought you had a better chance at succeeding and b) recognized how big an impact altruism probably has on your happiness.

I don't know how to feel about that.

For the record, I admire your honest attempts at introspection and truth.