Many people change the pedals and saddle soon after purchasing, but your mileage may vary.

You could have a chainguard installed, but in my experience, it's not particularly helpful. Just roll your pantleg up, or get a leg strap thing.

The stock brakes work fine. Short of replacing the front fork, I'm not aware of any way to fashion up a disc brake setup on a bike not meant for discs. I wouldn't bother.