Lynn, you have one of the best sites for affiliate marketing that I've ever seen. Just read your interview with Rosalind Gardner and found some interesting nuggets. Marketers should note the intuitive and spontaneous way you approached a niche and keywords. This is usually where "paralysis analysis" begins … some spend weeks with keyword and research tools until there is no "creative energy" left to build the site.
Google claims their users click (organic) search results more often than ads, essentially rebutting the research cited above. A 2012 Google study found that 81% of ad impressions and 66% of ad clicks happen when there is no associated organic search result on the first page. Research has shown that searchers may have a bias against ads, unless the ads are relevant to the searcher's need or intent 
And executives in particular, whether you’re getting help from an external coach like myself, or have an internal expert that can help them with their profile, this is really important because your executives are the key to really building thought leadership. I know even at Act-On, Bill Pierznik has been making some really amazing posts on LinkedIn around his thoughts on the business world, and it’s garnered a lot of engagement. So, the more you could have your executives be the voice for your company and really get their profiles up and running, the better.
Now in your reconsideration request make sure you are honest and tell Google everything that the prior agency was up too. Be sure to include all Excel information of removed links and say you are going to make an ongoing effort to remove everything negative. It is common knowledge that Google may not accept your first reconsideration request, so it may take a few times.
Because so few ordinary users (38% according to Pew Research Center) realized that many of the highest placed "results" on search engine results pages (SERPs) were ads, the search engine optimization industry began to distinguish between ads and natural results. The perspective among general users was that all results were, in fact, "results." So the qualifier "organic" was invented to distinguish non-ad search results from ads.
The home page of your site is usually a good place to start. It typically holds a wide array of information about your product or service and will lead the website visitor to where they want to go. However, if you have other informative pages on your site that you think would be more helpful, you may want to choose one of those pages in addition to, or instead of, the home page.
I agree with the point that a small or medium-sized business will have limits for budget and resources in generating brand search, but I wouldn't say that stops them from potentially producing huge growth there if they do something interesting/innovative etc. I can think of quite a few small to medium sized brands that have more name recognition than larger companies in their space. The challenge is that many of those brands are led by people who are very good at generating marketing and publicity - it's harder for small brands to be able to afford to pay for a top level consultant or agency.
Now, it is not that these sites are not interested in Google users. In fact, they have hired us to help them increase their share. However, they are getting so much traffic from sites like Facebook that it seems there is less urgency about attracting this traffic and less willingness to change the site to meet organic standards. Not long ago, sites would urgently and unquestioningly abide by Google’s standards to court that traffic.