Geneseed implantation is incredibly stressful on the human body, and women have frailer bodies on average. Less upper body strength etc., so that inevitably breaks immersion a bit, if you're forcing this incredibly risky surgery on people less capable of handling it.
It also introduces the topic of sex and how do you deal with this for space marines. Some people might like such an idea, others would prefer space marines to be penitent warrior monks.
But moreover, people are also worried about a shift in narrative, in themes. The narrative of many modern franchises is that of the outsider triumphant, that the new groups of people are saviors against their hated foes, that they are taking over the old machine, running it far better then the old guard could ever do, and the old guard are all foolish bigots for doubting them. Usually this is meant as a direct parallel to modern times, a reminder of the "need" of certain races/sexes etc. to submit to their betters.
Many people find such media insulting and humiliating, the same way a slave would be humiliated by being forced to watch a movie about how dumb he is. It doesn't matter how well made the movie is, the slave would rather not watch that movie.