I've also had poor luck with the built in flash with macro. Whether it's the TTL flash or the A setting, I find it often is drastically over-exposed, and that going to full manual flash and exposure is preferable. Especially if the subject is quite close, I may end up setting the flash to one of its lowest manual settings.
I get much better results with an off-camera flash. Of course on your camera as well as my D7100 this can be difficult, as there is no connection without an adapter on the hot shoe, but if you want to get more serious about macro I highly recommend this. You can find the SC-17 or later cords fairly inexpensively sometimes, and if you go on full manual mode in the camera, you can use almost any flash. There is no need to find a Nikon flash, or any recent TTL. It takes some experimentation, but a fully manual or old-style thyristor auto flash works very well for this. Much of the time you can just hand hold the flash gun without worrying about any mounting, or lay it on a table or the ground.
Once you have an off camera flash, you have a lot more control of shadows, background light, and so forth, and some of the modulation of light level can be as simple as just changing the distance of the flash gun from the subject.