Hi sept90,
the main thing about nuts and saddles is hardness. You want the material used to be as hard as possible.
Cheaper guitars tend to come with plastic nut/saddle. Plastic is very much softer compared to more expensive materials like bone, ivory, brass, etc. The 'softness' of plastic absorbs and cushions the vibrations of your strings. Hence, adversely affecting your 'tone'.
Popular alternatives to plastic would be bone, fossilized mammoth ivory(FMI) and TUSQ, which is synthetic ivory.
I find bone to be quite bright, and FMI to be a tad warmer. Tone is subjective, so I cannot guarantee you that it will sound better to you. But it widely acknowledged that bone/FMI/TUSQ sounds 'better' and will improve sustain and articulation.
When it comes to string-gauge, the thicker gauge always sound bigger, bolder and better.
Thicker strings have more mass, and they cause your acoustic guitar's top to vibrate a lot harder and better, as compared to thinner strings.
Better and more drastic vibrations on your acoustic = bigger, better tone.
However, some people might find thicker gauges more difficult to play with. Also, with the added tension, your acoustic guitar's top might not be able to take it as well.
Cedar tops especially, cannot take too heavy gauges. The maximum I'd recommend for cedar tops is a set of gauge 12s. For spruce tops, 13s are the max I'd advise. This is due to cedar being a much softer wood than spruce, which is a whole lot stiffer and stronger.
If you slap a set of 13s on a cedar top, you'd be likely to see a drastic bellying at the lower bout.(and I'm not taking humidity into consideration.)
Personally, I use gauge 12s. They are a good compromise between tone and playability and common sense.
Gauge 11s are undoubtedly easier to play but they sound too thinny.
13s are a big no-no as I don't want to put too much stress on my top.
12s are the way to go.