No, you didn't make a mistake if the camera is meeting your needs. The D90 has an advantage in terms of controls for someone who is more experienced, but the D5300 has an advantage in terms of sensor quality. So if you are pretty new and learning, a basic model that has fewer controls to confuse can actually be an advantage for now, particularly since, all other things being equal (and assuming you don't need to be able to adjust the settings quickly), it is capable of better looking photos (just a bit harder to use in the hands of an experienced user.)
Eventually you will find the lack of controls limiting, but at that point, you will understand what you are missing because you'll be looking for it and a camera with more advanced controls will be a help rather than a hindrance. (Also, note that you can adjust pretty much all the same settings, it is just that you have to go through menus for some things that are on direct controls on higher end models.)