Rashi, on 173a in explanation of "meshulashim" uses Yosef ben...Yaakov instead of the usual Yosef ben Shimon. Twice. Why the change?
The generations in the "Ben Yakov" example are well known. Using that system we can go up to four familiar generations, conveniently using "Avraham."
The Mishnah does not *name* more than the first two generations (i.e. Yosef and Shimon). The Rashbam, however, is interested in listing the names of the third generation and up, so ben Yakov is more convenient.
the yad Rama in igros at the end of sanhedrin says that these names were chosen because of a maasa shehaya.
Rav tzadok of lublin says other reasons.
Gilyonai hashass also speaks about this