#1
The treble notes on my classical guitar are little, how shall we say, lacklustre. Lacking in intensity, sustain and brightness. Part of the problem is just the break angle across the saddle: with a shallow break angle, the strings can squirm against the saddle, wasting energy. Now, I could modify the bridge, in fact I already tried that. I glued toothpicks inside the holes! Unfortunately, I used white glue since I figure it would be easier to undo if I screwed it up. The strings have now mostly pushed the toothpicks out of the way.

I'm considering a more serious modification, but there is an easier way: just cut notches in the saddle. This will prevent the strings from squirming around. Now I've done this before on a really, really cheap guitar and it worked: increasing both sustain and volume. I've also heard any number of times that it's a bad idea, but no well-reasoned explanation as to why. After some searching, I finally found a guy who recommended it. Well, I have finally done it on my reasonable quality student classical guitar (La Patrie Concert) and can now unequivocally say why it's a bad idea.

I'm just curious, does anyone else know?
#2
I'm not going to speak to nylon strung guitars, I have no experience with them.

But with steel strings, if the strings are crawling across the saddle, the neck of the guitar is set wrong, causing the necessity of the saddle being too low in the bridge.

The upper end of the neck being high in relation to the bridge, ultimately results in the saddle being too low, after adjusting the action to a playable level. That is what causes the shallow break angle. If that shallow break angle exists and the neck is set correctly, the bridge is likely malformed.

Another thing with steel strings, they generally cause a slight indent in the saddle after some playing. In other words, they file their own grooves.
#3
I agree with Cranky, it might be more involved than you think. You might try replacing the saddle, and having a greater break angle on same.... More angled from the side where the strings are tied.
Also....Are you using the proper technique for securing the strings? I mean, every once in a while, you may see someone tying them on wrong... Backwards or over the top of the bridge instead of from the hole.

Finally... There are high-tension nylon strings available. Dunno if they would help, but couldn't hurt.