I have 9 year old boy/girl twins and am heavily involved in a Cub Scout pack with both of them, so I have some perspective on Cub Scouting for girls. However, the Girl Scouting program in my town is not well-developed so I didn’t have much of a choice for my daughter.
My son started in first grade before girls were admitted to the program, but his twin sister tagged along to many of the events and enjoyed them. The next year, when girls were allowed to join, she did so enthusiastically. She’s an artsy, non-athletic, budding fashionista girl, but loves the program. I think she likes the focus on outdoor, real life skills. For instance, she was very excited about the knife safety/skills training module so she could get her own pocketknife.
The nice thing about Cub Scouts is that it is organized on a Pack/Den model, in which the Pack, consisting of Scouts from grades K through 6, meet and do activities together sometimes, and then a Den, consisting of Scouts from a single grade, meets separately. This gives some overall control and continuity at the Pack level, so it is not entirely based on who the Den Leader is. My understanding is that the Girl Scouts program is organized almost exclusively in grade level units.
My Pack is heavily majority male, though it is evening out in the lower grades. For instance my daughter is the only girl among the dozen third-graders. Technically, she is in her own Den (because boy and girl dens are supposed to be separate), but she meets with one of the boy Dens (which her brother is in). She really doesn’t mind, and has lots of fun with the other girls around her age at camp-outs and things.
My impression is that the Cub Scout program is a bit more rigid, with specific required activities/skills for each grade, as well as optional activities, with the Girl Scout program having more flexibility based on the interests of the individual leader (and, presumably, the girls).
Most of our Cub Scouts enjoy their uniforms, and the distinction of wearing them, My daughter is very into her official Cub Scout uniform skort, in addition to the unofficial leggings I got her and the Cub Scout necklace she saw and asked for when we went into the Scout Shop for Pinewood Derby materials (like pink wheels for her car). The Girl Scouts I see seem only to have felt vests, which may not have the same appeal.
In my Pack, which is very diverse religiously, the religious element is strongly de-emphasized. Basically, we tell the parents to do the religious activity with your child as you feel appropriate, and tell your Den Leader that you have done so.
All in all, they’re both great programs, though they depend heavily and can vary based on the adult leadership. I feel that the Cub Scout, and later the Scouts BSA (formerly Boy Scouts) program, may be a bit more organized and skills-based. However, the best thing to do is to check out the local programs for your daughter and see which she feels most comfortable in.
Good luck.