A lot of the startups YC doesn't fund aren't necessary bad, just too early. And while not getting into YC will never destroy your company, getting in too early actually will -- if you start the clock on your company while you are still missing some basic skills, if your founder and you later break up, if there are still too many technical/product uncertainties, etc.

If your idea isn't inherently bad then just peel away away some layers of risk and try again.