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Good idea or not, SOMEBODY will try to mess up the network (or co-opt it for their own use) sooner or later. They'll either hack the existing code or write their own version, and will be a menace to the network.
I admire the flexibility of the scripts-in-a-transaction scheme, but my evil little mind immediately starts to think of ways I might abuse it. I could encode all sorts of interesting information in the TxOut script, and if non-hacked clients validated-and-then-ignored those transactions it would be a useful covert broadcast communication channel.
That's a cool feature until it gets popular and somebody decides it would be fun to flood the payment network with millions of transactions to transfer the latest Lady Gaga video to all their friends...