I don't know about Nida and Shabbat, but as far as mesechet Taanit I heard a really interesting explanation.
I'm clearly not doing the explanation justice here, but in the Talmud Yerushalmi, Mesecht Taanit, is called mesechet Taniot. Because outside of Israel, you can not declare new fasts, and many of the fasts that were declared were optional based on historical circumstances. (i.e. Shmad) The Gemora in Taanit 11b or 12b says that "There are No communal fasts in Bavel save for Tisha B'Av" So in Bavel, only Tisha B'av was a fast which could be declared and kept on the public level for all generations, and so they renamed the messechet to Taanit, instead of Taaniot.
Ramban writes (as quoted in the Ran):
אין שם תענית ציבור בבבל אלא כל התעניות שמתענין בבבל אינן אלא כתענית
יחיד. לפיכך אינו אסור בחומר תענות צבור. והטעם מפני שהדיינין שלהם
הדיוטות הם ולא סמוכין ולא היה להם נשיא שתהא גזרתו קיימת על כל ישראל.
לפיכך כשהצבור מקבלין תענית צריכין לקבל כולן על עצמן כיחידים שכל אחד
מקבל על עצמו, ומשום הכי אינו חייב לנהוג בו אלא כתענית יחיד. אבל בארץ
ישראל שהיה להם נשיא, לא היו צריכין לקבל על עצמן לפי שגזירתו קיימת על
כולן וכולהו בתריה גרירי.
There are no communal fasts in Bavel; rather, all the fasts that they
observe in Bavel are merely individual fasts. Therefore, they are not
bound by the stringent prohibitions of a communal fast. And the reason
is because their judges are laypeople and do not have semichah
(rabbinical ordination)* and they did not have a nasi (president)
whose decree would be valid for all Israel. Therefore, when the
community accepts a fast, they all have to accept it upon themselves
as indivduals, everyone accepting it upon him/herself, and because of
this, they only have to behave as on an individual fast. But in the
land of Israel where they had a nasi, they would not have to accept it
upon themselves, because his decree is valid for all of them and they
all follow him.