Beckett is still a somewhat useful guide. Most of us know that somewhere around %50 of Beckett's value is what cards will sell for at shows. EBAY is anything but a price guide, simply because sales depend on a variety of factors. They include the quality of the listing, the end time and date, shill bidding, whether the card was listed shortly after product release or several days later (we all know early listings tend to bring higher dollars), shipping costs, location of the seller, etc.
Most experienced traders, buyers and sellers have a pretty good idea of a card's value without the use of a guide. The exceptions are old vintage and extremely short prints, those cards that are less common.
Beckett's biggest flaw is not so much the prices they list, but their inability to respond to a fluctuating market, especially the printed guide that appears every two months. They also seem to have a problem coordinating their on line pricing with their printed guide. I've found discrepancies many times that are not attributable to player performance or injury.
I don't think there is any simple solution to establishing a card's market value. Realizing of course that markets vary by location I believe value is established by negotiation.