I would say the analysis of the algorithm is somewhat simplistic, but the fact is that there are many possible ways to analyze any queueing algorithm, and having just two types of connections is good enough to show some of the behavior characteristics. The most interesting result here is that the queueing algorithm on its own is not the only important parameter; one must also take into account the flow control algorithm. In fact, queueing by itself does not "fix" network behavior; interaction with flow control is important.
Under FQ, using "generic" flow control gives you less than your fair share--- the authors frame this as an incentive, but a contrarian view could look at it as a weakness of the algorithm. I think a better algorithm would penalize "generic" flow control but would only penalize misbehaving hosts which do not perform flow control or try to overuse their fair share.
In addition, the authors say that under other scenarios result in confusing behavior; an example would be useful. Overall, the paper is good in showing that more sophisticated queueing and flow control can result in fairer service, but the large weakness here is that routers must perform quite a bit of work, including maintaining per-connection state, that may slow down the routing overall.
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