This is a fascinating question, in part because there are a number of different answers, any or all of which might be partially correct!

The easiest solution would be to say, "well, some people did call him 'Napoleon the Great,' but that epithet's use was heavily dependent on the political context of the time." We see shades of this, for example, in a Google Ngram for "Napoléon le Grand" in French texts from 1800-2017. As one might expect, usage of the phrase peaks around 1808; the local minimum in 1817 is, if a bit late, fully consistent with this explanation; and we see another period of activity begin in the later 1840s, around the time the future Napoleon III's political career came into full swing (he was elected President of France in 1848). While usage has been on a downwards trend since then, it hasn't reached the lows of the ~1820s, as successive republican governments leaned less heavily on censorship of Bonapartism than did the restored Bourbons. A bimodal distribution centering on the reigns of Napoleon I and Napoleon III is even more apparent in the Ngram for "Napoleon the Great" in Google's English-language corpus, where, as we can see, usage falls off much more heavily from the early 20th century on. (Why? I will confess I have absolutely no idea.)

Of course, you must keep in mind that the broad shape of the Ngram is generally useful for displaying the relative levels of use of a given phrase—in both cases here, if you look at the numbers on the left, the actual share of the corpus that uses it is rather small. That plays into explanation number two: royal epithets were already falling out of fashion by the early nineteenth century. Yes, it is true, most of the Bourbon monarchs before the revolution possessed one (the exception being, tellingly, Louis XVI); but then, 75% of them were named Louis! Napoleon I, by contrast, was Napoleon the only (if one ignores the largely on-paper reign of Napoleon II, as seems justifiable) until his nephew proclaimed the Second Empire in 1852, so disambiguation wasn't exactly needed.

More importantly, and here we return to point 1, "Napoleon the Great" still seems to have been more commonly used than the epithets of some of his contemporaries: compare, for example, the Ngram for William IV of the UK's epithet of the "Sailor King," and Napoleon's nickname is around an order of magnitude better represented. Again, we have to recognize some of the limits of the Ngram here, which also includes any sentence fragments including "Napoleon, the great [so-and-so]," and thus may be more broadly inclusive in that case than in that of the Sailor King; my point is only to illustrate broad trends.

Finally, as I vaguely gestured above, we might speculate as to the effect of the varying acceptance of Bonapartism as a political ideology. This is, unfortunately, the aspect of the question that I am least well equipped to delve into, so I'll leave it to another poster to explore.