They could have but they didn't. It still doesn't change the fact that they give her more height and that they literally have an application for zooming around with rockets. I don't know, I think that's way cooler than your standard jetpack personally. Trust me, I'd rather have her just be taller but I don't see them as problematic as other designs I've seen in this thread.
I personally have nothing about Samus' jet boots as a concept in Smash 4, I think they give her a few moves that are pretty cool. I find them the epitome of ugly (neon yellow? for real) and, well, they don't look like jet boots at all. All of that said, the notion that she would use them to intimidate her enemies may be the most unintentionally hilarious thing I've read in weeks. :)