Lesson well-learned about eBay. It will always flatten values. For serious collectors of rare and quality items, eBay must not be seen as the essential arbiter of resale and/or collectible value.
You are being very purist here. Ultimately, the market will set the resale/collectable value, and this will vary according to the market that you sell/buy in. Ebay has the enormous value of being convenient for a lot of people, but has the enormous drawback of netting so many pieces from around the world that values may be lower if the rarity value is less. However for the seller this may be offset by the fact that an item will sell comparitively quickly. For a very rare item, the value may in fact be higher, as the number of buyers competing for the item will be higher.
If a traditional land auction is chosen, then the price achieved will be lower for middle end items, as they are likely to be bought by a dealer who wishes to add his profit margin. Rarities will sell highly provided the auction house catalogues and advertises the piece well.
Alternatively, a seller can sell in a traditional retail environment, as many buyers do not like to buy remotely, but prefer to handle the goods and chat to the seller in person. The buyer has less choice as they have only the goods in their immediate vicinity, and so may choose to pay a premium price to get an item they want if it comes up close to home. For the seller, his fixed costs will impinge on his profit margin, and he may have to hold on to the item for some time (perhaps years) until the right buyer comes along. This obviously has also to be reflected in the price.
None of these differing price structures is wrong or right, they are each relative to their individual selling environment.