For folks that played MGS3 expecially, this is probably a no-brainer, but choosing the appropriate outfit and cardboard box types is integral to efficient stealth.

If you arrive in a mission area and you're getting spotted at a distance, evaluate your environment and get some new threads dropped in. The right outfit will make you essentially invisible while crawling. Check your foliage, soil coloration, geology, and consider potential points of cover.

Also, if it hasn't been mentioned elsewhere in this post, major locations have orange "delivery platforms"; by taking a packing label from these platforms, you can use them as fast travel points by hiding in your box on the platforms.