I know it sounds like the same old simple answer, but Practice!
I've noticed in my own cutting the difference a few years can make. Even on basic stuff. Just the other day I wanted a small box for something and decided on a modified smaller version of Steve's round Yin Yang box. I remembered having the pattern in my files, printed a copy, went to my shop and knocked it out in no time at all. When I finished I was thinking about how a few years ago I would have had to give each step some thought, and that each step would've taken twice as long. Plus, the pieces probably wouldn't have fit together so perfectly without adjustment. It was a gratifying though that I basically whipped it out on auto pilot.
Anyway, sorry for the long digression. My slotted items fit much better now than they used to and I think it's just time and repetition. In a perfect cut for slotted items, intarsia, or anything that needs a tight accurate fit, the cutting would split exactly half way into each line.
Many people cut right to the edge of the line, or sand to the line after cutting. That's fine for cutting any single piece. However, once you start fitting pieces together, if you leave the full line on both pieces, you in effect increase the size of the two pieces together by the amount equal to the width of the line. The fatter the printed lines, the greater the effect is. That's also why when I make a pattern I use the thinnest hairline lines that I can. especially for intarsia or fitting one piece into another.
Ray