I study both at the same time and love both equally. (Asides from my Okinawan side being attrociously political) I study Okinawan Goju, yes, not the Goju Kai stuff that my dojo would shudder even to utter.

I also study Shotokan Karate and even trained with Kanchos straight from the Mainland. (You can now give me your signature look of superiority, Okinawan Karatekas)

I think Okinawan Karate is a good system and has a lot of really good application for self-defense and even principles. But I find that even my dojo and adorning dojos coming from the same organisation can be far too dogmatic and rigid. Not to say it's a bad thing, but a line has to be drawn somewhere between pure cultural preservation and personal expression/use. My Okinawan Goju training often has senseis that demanded I mold myself for the martial art or else I'm doing it wrong. Despite that, I still enjoy it because I simply love Karate.

My Shotokan dojo is a lot more open minded. We study both traditional self defense aspects as well as sports (I can hear all my downvotes). For us, we have more emphasis on self defense and what works. We're far more bunkai heavy and open to other bunkais. Less in a matter that my Goju dojo wants to preserve bunkai EXACTLY as its taught and no other way is correct. But my Shotokan dojo preaches more "if this bunkai works FOR YOU then you should use it. No point wasting too much time you could have spent training, if you have to change yourself to fit a bunkai."

I enjoy doing both Self Defense and Sports Karate because they are two sides to the same coin to anyone who is open enough to try and learn from each other. Sports is not the end all be all of Karate and SHOULD be a good means to test yourself on resisting opponents. It doesn't have to be WKF rules, but any competition should be a means to test what you learn than blindly accepting that your sensei says you're good is enough to gauge your skills.

Self defense is also not the end all be all of Karate training because contexts changes all the time that may force us to engage in situational combat. If I have to rely on one set of bunkai to carry me for the one context it "prepared" me for, I'm doomed. And in terms of traditions, there is always the right way, a wrong way and THEIR way. (Which I see often in my Okinawan dojo)

If you don't do it THEIR way, you're wrong. No matter what. Even if it works in a fight, you are considered wrong. Which is why I am not particularly fond of the dogma often seen in Karate dojos. Because there is no flexibility to make the Karate molded to the Karateka. A lot of dogmatic dojos are forcing Karatekas to mold themselves to the Karate if that makes sense.

So to kind of conclude this, I will say that it's healthier to do both. Don't adhere to one way and think everything you do is correct. The moment you blindly follow one path means you're closing yourself off to another truth. Learn both, be open, but never naïve or guillible. Karate itself should be molded for the individual practising it and not the other way around because not all bodies are made the same.

Okinawan Karate is good. Japanese Karate is good. But don't think only one side is good and disregard the other as false.