When ebay raised their fees last year, AuctionBytes did an article discussing the effects on stores with several useful comments from leaders in the field, and links to other pertinent information. Pretty interesting reading: http://www.auctionbytes.com/cab/abu/y206/m07/abu0171/s02
Here's an article on search engine optimization for stores: http://www.auctionbytes.com/cab/abu/y206/m11/abu0178/s03
I think ebay needs to do more to promote the stores, instead of focusing their efforts so heavily toward the "core", or auction business. Search result placement (or 'non-placement') is a prime example of this mindset. Unless that happens, ebay is going to remain a tough selling environment for stores.