I think we're having trouble understanding your question, as you phrased it. I think what you're really asking is, why is the "emperor" of Japan (the monarch in Kyoto) called "emperor" while the military leader in Edo is referred to by his Japanese title - shogun?
There's a couple schools of thought on this. First, Japanese "emperors" always saw themselves as the peers of Chinese emperors. Japan adopted the Chinese political system back in the 7th and 8th centuries. The title of "tenno" or "heavenly sovereign" is similar to the Chinese emperor's title. And we generally have no problem calling Chinese emperors "emperor." So why not do the same with Japan.
Second school of thought is that - at least until 1868 - we shouldn't call Japanese emperors "emperor" because it's inaccurate. First, "emperor" derives from the Roman title of "imperator" which was like a military commander leading an army. Japanese emperors NEVER did this and kept their distance from military matters until modern times. Second, as you seem to hint at, for most of Japanese history real political power was held by court or warrior elites and not the "emperor." So what should we call the Japanese "emperor?" Many scholars now are just adopting the actual Japanese title of "Tenno" with a capital "t." Just as we freely use foreign titles untranslated - czar, sultan, caliph, emir, etc - why not "Tenno?"
OR, other new translations have been "Heavenly Sovereign," "Sovereign," "Monarch," "Great King." These translations are more accurately derived from various Japanese titles of the "emperor."
This issue of terminology became a problem in the 19th century when American diplomats began negotiations with the Shogun (or actually, the shogun's ministers - the shogun at the time was a moronic weakling). Americans of course had no idea what a "shogun" was and got confused when Tokugawa officials tried to explain the difference between the emperor and the shogun in Japan. Eventually they settled on calling the shogun "taikun" or "Great Prince." And, yes, that's how we get the word "tycoon."
When we get to the modern period after 1868, I think we should definitely refer to the Japanese emperors as, well, "emperors" for lots of reasons. But before 1868, take your pick.
Of course, we're so used to calling Japanese emperors "emperor" now that it might be less confusing to just keep things the way they are.
The Shogun and the Emperor are different entities. The Emperor of Japan comes from a long dynastic line that supposedly comes from the Sun Goddess Amaterasu and thus his role his permanent and sacred as he and his descendants are the leader of the Shinto religion. That said during the end of the Heinan period the actual power of the Emperor wained when the Kamakura bakufu was set up by Minamoto no Yoritomo who was the first person titled Shogun to have some more executive powers than the Emperor for the pure fact that they still served for the Emperor (the Emperor was more or less sheltered from the outside world and having to make any decisions yet they would appoint Shoguns that had de facto power acting "for the Emperor") and that with the rise of the samurai class, more power was able to be taken by Shoguns whose affairs were almost always tied to military matters and support from friendly clans, a part of policy the Emperor didn't get involved in but permitted more prestige and actual power.
The Shogunate fell with the Boshin War and rise of the Meiji Restoration restoring more power to the Emperor's office with a parliamentary set-up to make their government more in-line with western governments. The religious role and some executive roles of the Emperor diminished after WWII.
I don't see what you're referring to. tenno ("heavenly sovereign/emperor") means "Japanese emperor". It was also common in the 19th century to refer to the imperial court in the same way the Japanese would refer to the Chinese emperor (kotei).
The Chinese reading of the kanji for tenno would also have clear imperial connotations from the second character.
Definition of emperor in English A sovereign ruler of great power and rank, especially one ruling an empire.
Definition of shogun in English A hereditary commander-in-chief in feudal Japan. Because of the military power concentrated in his hands and the consequent weakness of the nominal head of state (the mikado or emperor), the shogun was generally the real ruler of the country until feudalism was abolished in 1867.
Basicly the Shogun was the actual ruler of Japan so when they translated the title they looked in the dictionary and saw that his position in power matched the definition of emperor in English.That and probably bacause the Japanese already called theyr figurehead ruler mikado (emperor) they desided to simply call the Atual person in power that.
I'm a bit confused by your question. Emperor is a title that does not necessarily imply more than ceremonial powers. Are you asking why the Shogun did not declare themselves Emperor of Japan?