For an organization that explicitly advertises itself as a morally driven environment, it's extremely hypocritical for it to have any level of an abuse problem (sexual or otherwise).
That being said, it's been having an identity crisis for years, far longer than the circa-2018/19 attention on getting them to allow women. Obviously, like school, all of the troops are difference and experience their own unique sets of issues.
I was in Boy Scouts from 2004 to 2010, and Cub Scouts before then (1999 to 2004). I suppose I was lucky to start my adventure with a pack and later troop that was located in a liberal and wealthy suburb of Chicago that counted many highly educated people among its population (right down the street from Fermilab).
By 1999, they'd already started allowing women to participate as leaders. My den leader was a woman, many of the instructors were women. Cub Scouts (at least my experience with it) didn't have the same religious aspect that the boy scouts did. Our pack was chartered with a school, in contrast to Boy Scouts which typically charters with a religious organization (church, mosque, synagogue, etc.).
The actual material in the handbook and the overall organization has been ever increasingly non-denominational and non-christian-specific for years. While it wasn't explicitly accepting of atheists or agnostics, most troops don't really care that much about it. Religious service is not a required part of the activities, and by 2010 it'd been watered down to the point that you could barely recognize that you're participating. I was openly agnostic in my troop in Alabama. Moms were also openly encouraged to participate as leaders in the troops I was in. My mom was the backpacking merit badge counselor among other outdoor and survivalist activities.
The whole "exclusion of young women and homosexuals" sentiment can be taken a few ways. Obviously in 2022 it's a lamentable position. It's definitely rooted in the very American religious theme that sex before marriage is bad, therefore anyone who creates a situation where it's possible is also bad. So in order to avoid temptation, you must separate the sexes. Homosexuality turns that on its head because the boys can be attracted to the other boys.
No one had an answer how to resolve concerns, so no one changed anything. When the social progressive movement really got off the ground in the late '10s and was flagrantly demanding sweeping and immediate change to long-standing groups, they were kind of blindsided. Venture crew was a co-ed organization that allowed women to access the Boy Scout high adventure camps, but Girl Scouts was not an equivalent organization to BSA. It has a lot less national direction and troops were very different. Some of my coworkers in California have their daughters in it, and they sound like their having a similar experience to what I had in Boy Scouts. However, when my sisters went in Alabama, they were trying to turn them into proper southern housewives. Hence why they tagged along with my troop as "honorary Boy Scouts".
The appropriation of Native American culture other comments mentioned is also lamentable, at least the part where "white suburban dads jump around in costumes". For the most part it's not too bad, most of the call outs use their culture as an example of one that was more respectful of nature, in contrast with the European colonial worldview the US was largely embraced in their interactions with the Native Americans.