While I find the raise in waifu pandering to be annoying, I'm not to worried about it, it's definitely a passing phase. There will always be people who want original, meaningful plots and characters in their shows and that will inevitably mean including little boys in your cast. It may not be a large amount, but they'll at least be quality, and they will be there.
I've personally never been able to watch kid marketing shows for more than an episode or two, which has unfortunately locked me out of a lot of popular shotas. But even with that handicap I still have gained a number from animes over recent years that I like.
What really troubles me is the decreasing number of shota in videogames. I play videogames a lot more than watch anime and that's where most of my favorite shotas come from. Unlike anime, videogames can get away with all female cast a lot easier than anime, because the story and characters don't have to be in the spotlight as long. They can supplement the boring setting with gameplay, which means that the all female fad is likely to stay around longer for games, as long as waifufags keep buying them and the panty dlc's. Unlike anime, videogames don't need character variety, and that scares me because that means devs have to actually want to put shota characters in.
Luckily through all this I've also seen a rise in fujoshi pandering in recent years, with each anime season having more animes aimed at them and more otome games being released. Most of them are garbage, but if japan is starting to see a market in them, it can't be long until they start to see the market in shotacons. The coming years could either be a barren wasteland full of shotacon suicide, or the golden age for us.
Fingers crossed!