I've been playing for a few years, very on and off. Dust in the wind is one of the songs I'm playing, but the travis picking just never sounds right. I'm self taught so upon studying a few tutorials, I noticed I learned a few bad habits - I would use my index finger on the second base note, instead of letting the thumb play both base notes, like I'm supposed to - and also, I learned to plant my pinkie on the guitar for stability, which I learned is a bad habit (because of less flexibility in the hand).

I've worked on these bad habits, but since I was doing it for so long, it was almost like learning the song all over again. I'm able to play faster now and the rhythm sounds better, but something is still just not right.

I'm trying to focus solely on the picking pattern now when I practice, without playing any chords. But I notice that after a little while, when I increase the speed, it just sounds wrong. I notice that even though I stopped planting the pinkie on the guitar, I tend to point it slightly outwards while playing, which seems to make my hand less flexible and tire faster. When I notice and I tuck it in again, it seems to improve my rhythm. Could I be onto something here?

I've watched several videos on travis picking, and tutorials for Dust in the wind, but they never seem to pay attention to small details like these. So I wonder if anyone could help me out with some tips on how to make sure I get the picking right without developing more bad habits and slowing down my learning?
I'm a Travis picker, though I prefer to call it alternating bass, as mine is descended from John Hurt, not Merle Travis.

Three suggestions;

Use a sound editor to slow it dwon so you can hear exactly what is going on:

Think of it as a mixture of pinches (thumb and finger together) and alternates (fingers playing notes that alternate with the thumb.

Try and find some (decent!)tab that shows you what is going on.

FWIW, I don't try and do exact copies, just "ïn the style of".
Quote by Desko
and also, I learned to plant my pinkie on the guitar for stability, which I learned is a bad habit (because of less flexibility in the hand).

That's kind of a thing that classical guitarists like to say but it isn't a bad habit at all and in fact on many other fingerpicked instruments is considered proper technique.
There's no such thing; there never was. Where I am going you cannot follow me now.
Thanks for the replies, I just watched some youtubes about proper finger picking technique, and in one of them I learned that the knuckles should always be the highest point, and the wrist the lowest point? I made a video of me playing and I noticed that with me, it's the opposite... the angle of my arm etc seems different too, I wish I could just find a really thorough tutorial on how to position and play, but they all seem to just jump ahead to the actual playing, and skip details like those.
Have a close look at how classical players hold their picking hand, it isvery efficient ergonomically. This is a pic of me, and it is close to classical posture:

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I happen to be using a thumbpick in this one, but it would look very similar if I was using my nail.

Note that my wrist is almost straight.
Looks like your hand is coming down from the top, my hand comes in more from the side, parallel to the strings? I should probably add that I have pretty long arms. I just can't find a way to hold the guitar comfortably unless I hold it like that, and I think I bend my wrist upwards to pick above the sound hole, if I straighten out my wrist and keep it low, I will pick further up the neck, away from the sound hole.