Why is it that many names of Tanoim and Amoroim are not commonly used? These were big Tzadikkim yet their names are almost unheard of. For example Tarfon, Chisda, Pupa, Avtalion, etc.
In general, names go in and out of fashion. Consider how today Avraham, Moshe, and David are common names, but we find only one example of each in the Gemara (respectively: Gittin 50a [actually it's given as Avram], Bava Basra 174b/Erchin 23a, and Yevamos 115b according to the Rosh's version). In fact, from Moshe Rabbeinu I don't think we find another Moshe (except for the one mentioned in the Gemara) until R' Moshe Gaon, in the 9th century.
So in the same way, it could simply be that some Aramaic names (for example, Abba) stayed in fashion, while others (such as Chisda) didn't. As another example, I see where the name Huna was in use among German Jewry in the 18th and early 19th centuries (in Bayreuth and Hamburg), but I've never heard of it being used nowadays.
I've heard it quoted in the name of R' Avigdor Miller that many names in the Talmud were nicknames or derivations of Hebrew names -- e.g. "Ashi" from Yishaya. Some are clearly nicknames -- "Issi" was a form of "Yosef."
Probably for the same reason you won't find too many Velvels and Berels in Yemen, or Saadias and Rahamims in New Square.
One of the great Tanna'im was Rabbi Yishmael. Unfortunately, a few centuries later, the descendants of the Biblical Yishmael were violently converted to a new "Abrahamic" religion.
From that point on, the name Yishmael was associated with that religion, so that even someone who may descend from this holy Tanna won't name his Jewish son Yishmael.