I've had my Surface Pro 3 since this christmas, and also have been experiencing these wavy/jagged lines.
One thing I wanted to report on that I haven't really seen mentioned in this forum often is that I have found the issue seems to be closely tied with palm rejection. I can't say if this is the same for everyones device, but on my own Surface Pro 3, keeping my palm off the screen makes diagonal lines nearly smooth, as if there is no problem at all.
Furthermore, on my own device, something I found that's even weirder. If I hold the backside of my device while I'm inking with my palm still on the screen, the problem also is also heavily reduced.
Here's an image of inking diagonally on my Surface Pro 3. Note that I used a ruler to make sure any deviation is due to the device itself.
I went to the Microsoft store a couple of weeks ago to see if the SP3's there had the same problem, and of the devices that I tried they all seemed to have the issue.
Is there anyone else on this thread who can confirm that this problem does/does not affect their device in this way? I find it very strange that putting my hand on the back of my surface would help the inking to the degree that it has