I've worked pretty much exclusively on the "back end" of development (research, proposals, reporting, no implementation), so my comment is only informed by that limited experience. I see a lot of proposals and reports -- therefore project structures -- that only consider gender as an afterthought. It's an extra section to add to a proposal so that the donor feels good that you're thinking about it, but rarely goes beyond "we'll make sure to include or target women in this project and disaggregate our indicators by gender." I can count on one hand the number of times I've seen project design take into full account what it means to address the unique needs of women, girls, men, and boys individually and together, with all its implications and context-specificity, and the sustainability of such cultural shifts, and I don't believe I've seen any project design actually reach a state of full gender mainstreaming (maybe one).
But, to be fair, I think this is a systemic issue that our field just hasn't been able to tackle yet. Gender specialists cost money that often organizations cannot afford to spend if covered by overhead. They can't justify the cost because gender specialists often are not needed to win awards. Most RFPs and proposals don't seem to be written with strong oversight from gender specialists (not just input) and don't seem to require gender mainstreaming. This isn't implementers' faults. This issue must be solved from the top down. If donors don't prioritize gender mainstreaming by making sure that projects are designed in such a way that achieves this and by allocating funding to cover gender mainstreaming at all levels, the field is less likely to take prudent strides to solve this issue.
Practically speaking, at the end of the day, we have to go where the money is to stay alive and the money doesn't yet seem to be with gender equity/equality/mainstreaming.