Admittedly I had a client with this. He was on Shopify. We did everything thgat franze highlighted. We did a full screamingfrog audit of the sitemap, and fixed everything from title length down to html and script problems. Wound up being really toxic backlinks that we needed to disavow. It still took a few months but finally his links were listing. The crazy thing is we had cloned competitors getting higher ranking before.