'Natural' reads are just guesses.
If you want to get better at reading, hop into any match, local or online, play very passively, and just watch. Try throwing out a move and watch for what their response is. Are they airdodging every time i get them in the air? Does that ROB always shoot a laser at me when trying to recover offstage? Is that Toon Link always throwing a bomb and following up with Fair?
Basically, just observe. When you see the same thing twice, make a note of it. Three times, and you can reasonably assume they'll do it a fourth time in a similar scenario. Then, use that knowledge to punish. I main Falcon, you see, so reads are critical to my success. I'll spend the first stock spamming Uair and Jabbing to do what is called 'conditioning'. Now the opponent sees this, and will preemptively airdodge off of a dthrow to avoid the seemingly inevitable Uair, as well as shield any time i'm in jabbing distance. Now that I see him doing this, the next time I walk up to him and without hesitation grab him, predicting that he will be in shield. I then Dthrow him. I will now shorthop jump and wait for the airdodge, which I also predict. As soon as I see it, he's doomed. Knee to the face while he's in endlag.
TL;DR get used to observing, and once you've seen a lot you can begin to start matches making reads just based off things you've seen other people using that character do.