@Shatner probably my last post.
First, it is a threshold. You won't have to fix 100% of your problems to recover.
Second, by fixing these issues, you will be stronger than before. Your whole site wasn't punished before, but these dupe pages never ranked before anyway. Fix them, they will rank where they once never did, and you will rescue all the pages that did rank before. You will be stronger.
Third, for myself, I threw away 2.4 million URLs by removing them from my coveted domain onto a couple other domains, and no-indexing the whole lot. They were all scraped anyway from more than 10 years ago when I sold books. I walked away from those 2.4 million URLs, they haven't put serious bread on my table anyway for more than 7 years. So, I don't have 2.5 million URLs to worry about, my new starting position is 100,000, and tons of that is safe (unique products, unique content, ranking #1 for the content). But I still have lots of dupes in there too, some my fault, some unfair, but who cares - I have some problems. They will be fixed.
Fourth, your domain may have intrinsic value. It may be pandalized, but it may still have value beyond what a new domain may have. This is not a penalty per se, this is recoverable - it is re-ranking. The value of your old domain far outweighs the value of any new start-again domain, especially if you have 100,000 URLs on it. Links, age, branding, etc.
Fifth, I am not pranking you. I am paying it forward. I have been helped in the past by members of this forum way beyond the help I could ever repay to anyone. But my altruism only runs so deep. ; ) I too must be pragmatic. ; ) I have to feed my family, and it is not lost on me that the more people who take my advice to heart, the more competition I will eventually have. ; ) Half joking, but, half serious too... ;) So, I have paid a tiny fraction of the forward I need to pay here by opening my mouth now, but... you can lead a horse to water, but you cannot force it to drink. ; )
Fifth, you say it took you 5 years to do 100,000 pages. Surely, you do not need to redo all 100,000 pages? Meanwhile, some of those pages are still creating some revenue for you. You are not down to 0%. I would rather start from 50% down, and work my way back up, than try to restart at 0% and try to work my way back up to my former 100%. I also find it easier to rework content, than to start with a completely blank canvas. I do not relish the thought of rewriting 5,000 pages of content, but I cannot fathom the thought of recreating 100,000 pages of content.
Sixth, everyone's situation is different, but my domain is more than 10 years old, and it is a "brand". I am also insulated in that I have multiple domains older than 10 years. As much as the task before me is daunting, killing this particular domain is not an option, when I weigh the pros against the cons, and consider all the value this domain has. Much easier to rework some content, than start from scratch. My infrastructure is awesome, I just need to do a search-and-destroy on dupe content - this is a much narrower task. I'd rather spend 3 months rewriting 5000 pages on an established domain, than spend 5 years recreating 100,000 pages from scratch AND start a domain from scratch.
In summary, I've done a small pay-it-forward here. A tiny, minute fraction of what I owe to all the white knights who've helped me in the past. ; ) For you, and for the multitudes of lurkers. For some I will prove to be the voice of reason, they will listen and consider, take a long walk to sort out their thoughts, then return and get organized and get down to work, and then thank me for it silently weeks/months from now. Others, well... I cannot save the world.
I wish you and everyone else all the best.
As for myself, I need to get back to work.