Honesty, I wouldnt approach the problem with a "whats her worse matchup?" mentality. I have literally no problems fighting the likes of falco, doc, or shiek, mainly because I made it a point to learn those matchups and what to take advantage of/what not to do. For example, having a reflector by no means insures that your match will be easier since, against a good Samus you will get baited and grabbed or punished in some other way. My hardest matchup currently is a good Rosalina which is mainly due to her hitboxes, and not at all due to the fact that Luma blocks projectiles, which is what most people reference as far as why that MU is hard for Samus.
The thing is that when you fight a good Samus, you are really fighting a wild card with an amazing projectile (cs), but also a killer dropzone game, since she can be played many different ways. Moreover, if someone IS in fact a good Samus player they are likely to be similar to someone training with weights on only to take them off when presented with a challenge. She has a lot of weaknesses that CAN be overcome but you have to know her inside and out to overcome them resulting in a much higher skill curve than, say, diddy kong. The best thing is to be adaptable in the heat of battle and dont underestimate her.