And why did Yakov put the sticks for the Mekusharos, but not for the Atufim?
Ramban: Had he put sticks for all of them, Lavan would have ended up with nothing. 1
Redak (also cited in Ramban): Even though he put sticks only for his own animals, if Lavan saw so, he would suspect that he did so also for Lavan's. Yakov did so only for the minority 2 that conceive early; Lavan would come to check only for the majority, which conceive late. 3
Rashbam (41): He did so for the Mekusharos, i.e. the majority 4 that become pregnant early. He was not concerned for the Atufim, which become pregnant later.
Moshav Zekenim (37): Yakov used sticks to tie his animals (make them Mekusharos), lest they mate with Lavan's. There was no concern for Atufim (sheep totally covered to protect their wool), which cannot mate. Refer to 30:37:1:7.
Tosfos ha'Shalem (40:4): Atufim would give birth by themselves. He needed to use sticks in order that the Mekusharos would give birth. 5
Ohr Zaru'a (1:769): He did not put for the Atufim, which were of Lavan, lest he uproot Lavan's property.
Ohr ha'Chayim: Normally, a shepherd gets only a third 6 of the animals born (refer to 29:15:152:2). We must say that without the sticks, some of the Mekusharos would not give birth to similar animals (with the appearances Yakov receives), or Yakov deserved to get more due to other thefts of Lavan.
He preferred to put for the Mekusharos, for they are the majority (according to Rashbam 41), or they are stronger (PF).
This is unlike Rashbam (41), who says that most are Mekusharos.
Perhaps also Seforno (Pasuk 40) explains like this. (He connotes that concern for suspicion applied only to the Atufim.)
This is unlike Redak, who says that most are Atufim.
This shows that he did not intend to make them give birth spotted. If so, he would have done so for all of them!
Ohr Yakar, in Likutei Ha'aros: The text should say 'half'. Segulas Moshe (in Likutei Ha'aros) - Mekusharos are worth more, and they were the majority. (Ohr ha'Chayim initially assumed that even without sticks, all babies of Mekusharos would be Yakov's, i.e. Mekusharos have the appearances that Yakov receives (refer to 30:42:1:8). If so, why are they worth more? And what is the source that they were the majority?