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Your SEO firm is probably correct, in my opinion. Having an overly high percentage of your anchor texts be keywords is one of the factors that makes your site likely to get penalized by Penguin or other algorithmic penalties. See http://searchenginewatch.com/article/2172839/Google-Penguin-Update-Impact-of-Anchor-Text-Diversity-Link-Relevancy Your SEO firm has most likely determined that your backlink profile uses too many keyword anchor texts, and they are trying to fix the unbalance by building mostly non-keyword anchor texts for awhile. In other words, they are trying to dilute your too-keyword-focused anchor text portfolio. Here are two more articles you may find helpful: http://www.searchenginejournal.com/anchor-text-optimization-case-study-whats-natural/43404/ (written by yours truly) http://www.seomoz.org/blog/anchor-text-distribution-avoiding-over-optimization

I agree with EGOL on this one... keep it all under one roof.  If you're looking for SEO value on the mini sites, why not turn them into landers that point back to your main site instead of the other way around?