Matrix could be a good solution, though that only works if the services actually support it for activation and verification.
Which ultimately is the problem with any alternative to email, they need to be supported by other services to be any useful.
I think the signup issues are mostly due to inexperienced admins not knowing how or that they can set up automated moderation for spam, or just not configuring their email server correctly.
Once we have better Anti-spam tooling that is more user-friendly it’ll be easier to get people onboard, and really only specialized niche instances should be using the application process, otherwise it does hinder growth and openness as a community. Already talked about this in my other comment but it is not good for Lemmy or the Fediverse as a whole to treat every instance like a club with applications to sign up, it limits people and makes it harder for normies to join, which needs to happen otherwise communities lack the life and activity they otherwise would and it becomes less useful as a social platform.