I've always had a few gripes about the scouting program within the church. First, it's expensive. Scout camp fees, badges, uniforms, books, equipment, and more tax ward budgets, and even with fundraisers, the families of scouts often have to lend extra financial support. Then, on top of all this, we run "Friends of Scouting" campaigns to raise money, not for our own boys, but for the BSA corporate structure. Each council has paid executives who need this money to fund their paychecks and run their offices.
Second, the path to eagle lacks flexibility. Most of the merit badges you need are not negotiable. While some, like personal management and physical fitness can be seen as valid life skills, others like camping, environmental science, and swimming don't appeal to all boys, and don't seem necessary in a program preparing boys for missionary service. With all the merit badges available, why are there so few electives in the path to eagle?
Third, there is no equivalent program for girls. Girls camp may be a fun program, but it lacks the structure, award system, activity opportunities, leadership training, and general recognition of the scouting program.
Fourth, the international church doesn't have the same program. A majority of church membership lives in areas outside the BSA's footprint.
Finally, the scouting program's requirements for leadership don't perfectly match the church's. I've read of active temple attending members who happen to be gay being called as scout leaders and having their assignment shot down by the scouting program at the council level. Yes, it's a rare circumstance, but a small problem can still sting.
Now, the scouts have done something interesting. They remedied my fifth concern, but in doing so they broke faith with church leaders by voting when they were absent. That might open a can of worms, because now the church is reviewing their relationship with the scouts. I don't see the vote itself as a deal-breaker between the church and the scouts, but if the review starts considering other concerns like those I've listed, the overall picture might incline leaders to sever the relationship. It will be interesting to see how this unfolds.