Here is my take on the AFA phenomenon:
I used to collect baseball cards when I was a kid and into my teen years. My friends and I would trade for what we though was valuable to us. When Beckett the magazine came out it started to put a value on what they thought were the market value of cards. Each month we would buy the magazine and see what cards were declining or getting hot. This made trading very equitable for both sides because you could see what your cards were worth.
Then the grading system hit!! At first, only the very special cards were actually graded, like a Griffey UD Rookie or older rookie cards. Then everything seemed to need to be graded!! Since when was a 1990 Wade Boggs graded U90 worth more than a Tony Gwynn ungraded rookie card that to the eye is perfect? I had enough and stopped collecting when I could not afford the packs any longer.
How does this relate to AFA gi joe? I would say that to some having their items graded by a third party system insures they know the items condition in relation to any other like item having gone through the same grading system. But!! That by no means provides a real value to your item. For instance, I see some auctions which state "only 1 of 2 graded", so that gives a perception of rarity. Well what if everyone who has this item starts to send theirs in to be graded. Some of those items will fall into the above category and then your "1 of 2" will be "1 of 100" So the more AFA grades and collects your money, the lower your value for the item becomes!!
I saw a silver pad grand slam sell for over $3K this week, AFA graded. In my opinion, when buying AFA from ebay, you are buying at the top of the market always and will never have your items appreciate. I would rather rely on the old supply and demand theory, not have it manipulated for profit by a third party, then sell it as a way to preserve the value of your collectible. Or as a collector, would rather own all the gi joes from 1982-1994 loose and complete, rather than one AFA graded silver pad grand slam!!