I have been a member of r/NASCAR for nearly a decade, and it's been a great place to gather with NASCAR fans outside of the stereotypical Facebook/Twitter crowd. Niche (ish?) sport/hobby/interest subs like that are going to suffer the most from reddit's potential downfall, as there isn't another viable, easily-accessible place for members of those communities to gather online.
The two biggest issues I've heard brought up (other than the fact that apps like Apollo just work better than the official app and don't have ads) is that moderation tools are dependent upon third-party apps, and third-party apps are more accessible for people with disabilities than the official reddit app.
This is what the protest should have been from the start. The biggest mistake that any of the participating subs made was setting an end date. u/spez and the rest of the reddit admin need to be sweating, wondering when their site will return to normal.