I feel we can also focus a lot on the kind of keywords we target. I had a client who was in a very competitive market place, we optimized their site for some really targeted, long tailed keywords which didn’t have very high search volume, so the traffic didn’t really go up drastically but the amount of conversions & the kind of CTRs the site received was incredible.
I think it has become harder and harder for smaller brands to really stand out in any kind of search. This is especially true with small brands who face lots of competition form other small brands in large cities. How does one build name recognition in NYC as an acupuncturists when any given building may house 3 or 4 practitioners with the same address. Then these small businesses are facing the Google Possum filter. And in some cases brands without websites are showing up in the three pack over highly optimized websites.
Regarding Link Detox, links it diagnoses as Toxic are generally fine as they're either not indexed by Google or have malware/viruses/etc., but I recommend a manual review of any diagnosed as Suspicious. I used it recently to get started cleaning up our backlinks and some legit sites and blogs were under Suspicious simply because they didn't have many links pointing to them.
Remember when you used to rely solely on search engines for traffic? Remember when you worked on SEO and lived and died by your placement in Google? Were you #1? Assured success. Well, okay, maybe not assured. Success only came if the keywords were relevant to your site users, but it was the only real roadmap to generating site traffic and revenue.