Another challenge is the risk of alienating one market is always present. To use the eBay example, they've recently focused their efforts much more squarely on buyers by introducing new "top-rated seller" criteria and a fairly liberal Buyer Protection Program. Buyers have benefited greatly, often at the expense of sellers. I imagine in the next couple of years, the balance will have shifted back to appease the unhappy sellers.

To contrast, Amazon seems to have done a good job of growing out its base of satisfied external sellers (no personal experience, just anectodal). Perhaps aiding this is the fact that Amazon has an intimate understanding of how to succeed as a seller (they get fulfillment, pain points in the purchasing process, etc.). They worked to cultivate their main market (the buyers), while actively operating in their future market (as a seller).