The greater stance depth in Japanese styles of karate (like Shotokan) versus Okinawan styles is also at least partially attributable to the manner in which Funakoshi Sensei promulgated his style: university physical education classes. To this day, there is, in many respects, a somewhat greater emphasis on "physical training" in Shotokan than in, say, Shito-Ryu. My personal experience with Shotokan is that I found the depth of stance beneficial for strength and flexibility, and for training purposes. (Kind of like the Roman legions used to train with 20 pound swords, but fight with 10 pounders.) That said, I think an additional by-product of this emphasis touches on your original question related to bunkai, and that is that many Shotokan schools are often less focused on the variety of bunkai, henka and oyo that can be applied through each technique in a kata, and more focused on stance training. (That may be why it seems that the bunkai you are being taught only work under strictly controlled conditions, if I may paraphrase.) Having come through Shito-Ryu, Shotokan, and now Shindo Jinen Ryu, I appreciate what Shotokan has to offer, but consider it a somewhat incomplete style with regard to kata. (And that is not because of inferior teaching either; I trained in both Okazaki Sensei and Mori Sensei's organizations.) Once you make some progress in your current style, it might be worthwhile to check out some cross-training opportunities like multi-style seminars to gain some additional understanding and experience.
