What you see as "an annoying little problem", I see as a sign that the system is consistent and robust. It's a good thing that the system doesn't distinguish between a hundred one-share orders and a single hundred-share order; such a distinction would be totally arbitrary. (By contrast, ranking orders by time is not arbitrary. All else being equal, it's better for things to get resolved faster; the only question is whether we're giving too much of a reward for too little of an improvement.)
Elsewhere in this thread (http://news.ycombinator.com/item?id=3856015) I argue against treating orders differently based on the "entity" that placed them.
In general, we want traders to spend their time thinking about asset prices and risk, not market structure and game theory. The price-time priority system is a very simple one that rewards traders for deciding what they want and then announcing it right away. All the modifications that have been proposed in this thread encourage traders to play games, second-guess one another, or otherwise work around the system.
There are definitely tradeoffs, but personally I think it's better to use the cleaner system and accept the latency arms race than to add a layer of artificial incentives -- and for what it's worth, it appears that nearly every major electronic market has come to the same conclusion.
Finally, thanks for the link to the Talmud article: it was a very cool application of game theory to history. (Of course, I don't see any indication in the article that the Talmudic system would be an improvement over pro rata.)