Another likely reason is the fact that most miners use pools to mine. As a result (with the exception of eligius), the found block will have the block subsidy "deposited" into the pool address, and when it is time to pay the miners the reward will be transferred to the miner's address.
Bravo! I've been seeing that graph posted for a while now and you are the only one that actually realizes what's going on. The reason an outside entity like MIT can't just grab the Blockchain and start analyzing transactions is because they really don't know how Bitcoin works or have any involvement in the community of users. It was probably some grad students class paper and he was "guided" (and I'm using the term loosely) by an even more clueless professor.
That would still give you a massively incomplete picture.
At one point I was mining at three pools at once. I learned not put all my eggs in one basket the first time Deepbit was DDoS'd. I was mining at Graet's pool, Tycho's pool and Slushes pool at the same time. I moved the coin to three different addresses every day to keep track of my earnings. Once a week I moved all of it to one of four cold storage addresses which I kept evenly balanced. I also kept some coin for almost two years at three different exchanges moving it in and out. I was mining LTC and Namecoin for a while on the free CPUs and selling the Namecoin for BTC at CryptoXchange and the LTC at BTCe for BTC and moving that coin to a separate address to keep track of that amount. I was trading heavily at BTCe and moving coins in and out of BTCe almost daily. I've moved coin in and out of Tradehill multiple times in a short period of time. I also had investments that paid dividends and moved that coin around. In one month I moved 1800 BTC between four addresses to set up permanent cold storage for them. I kept a separate address that I used for SpendBitcoin Amazon cards to replace failed hardware. I never mixed coins so I won't even get into that. Are you starting to get the idea that tracking addresses doesn't show expenditures?
I would argue that tracking addresses does not show economic expenditures. As you stated above it is possible to move your own coins around and it would be difficult to know if you are sending the bitcoin to yourself or if you are spending it (as in giving someone bitcoin and receiving either fiat or goods/services in return).
You may be able to devise some kind of way to monitor the economy but tracking addresses would be the absolute worst way. I can see tracking business sales directly as the best way, if you can get the data. I didn't even mention the times I sold a few coins locally through in person exchange. That's not a transfer for goods or services any more than all of the day traders and hobby speculators are. I'd be willing to bet that a good chunk of the $1.6 million Overstock reported in Bitcoin sales were miners replacing failed equipment or buying new cabling and equipment to make more coin just like I used to do at Amazon. Which is just a return to more mining not the support for a thriving economy. But how do you really tell? I can't think of a way.