Yishmael is a different story. Why?
Before Yaakov Avinu passed away he blessed his sons. This started not with his direct sons, but with his grandsons Efraim and Menashe. When doing this he crosses his arms so that his strong hand would be on Efraim, the younger brothers head. When asked why he explained that Efraim’s descendants will be more righteous than his older brother Menashe’s. The situation is still quite strange because the Midrash Rabbah tells us that Hashem saved Yishmael from the desert because he does not judge people for what their descendants will do. Furthermore it obviously mattered to Yosef and probably mattered to Menashe as well. Was it really worth it to honor the younger brother for what his descendants would be like?
Let’s take a look at what the Bracha was about:
“The Angel who has redeemed me from all harm— Bless the lads. In them may my name be recalled, And the names of my fathers Abraham and Isaac, And may they be teeming multitudes upon the earth.” So Yaakov is blessing Efraim and Menashe that their names should be connected to those of the Avot. This is in sharp contrast to what he later tells Shimon and Levi: “Let not my person be included in their council, Let not my being be counted in their assembly. For when angry they slay men, And when pleased they maim oxen.” Here Yaakov is saying that he does not want his name connected to the actions of the descendants of Shimon and Levi. Rashi says that this refers to specific cases: Kozbi, a descendant of Shimon who publicly took a Midianite woman and Korach, a descendant of Levi who started a rebellion against Moshe Rabenu.
It seems that Yaakov connects the actions of Shimon and Levi to those of his descendants. The power to avoid these situations was in the hands of Shimon and Levi. Just like Yaakov was able to anticipate which of his son will have descendants that would play large roles in extreme defiance of the will of Hashem, he was able to see which of Yosef’s sons was to be greater. The honor he gave to Efraim wasn’t for his descendants, but for being someone whose descendants will be great. We need to look at our lives and find not only where we’re going, but where we’re leading our descendants and our followers.
This does not apply though to what we mentioned about Yishmael, because although he was not a good person himself and in a way he is responsible for what his nation does, he wasn’t liable for what his children would do in the future. There it was a question of punishment and that’s where the line passes. Yaakov didn't punish Shimon and Levi for what their children will do; he disconnected his name not from them, rather from their rebellious sons.