Other factors maybe more important. For example, the risk of missing the connection, and the penalty of missing the connection can make a difference.

If your choice is A->B1->C and A->B2->C with similar connection times, but:
* A->B1 is frequently delayed.
* B1->C is infrequent, so missing it means the next flight is the next day.
* A->B2 is rarely delayed.
* B2->C is frequent, so missing it means perhaps an hour or two delay.
Then A->B2->C is a much less risky choice.

Also, if the itinerary is international, consider whether there are differences in doing immigration and/or customs at the connection stop, which can make a realistic-looking connection time tighter if that is the case.