More efficient programming probably has a lot to do with it. If the software contains endgame tables, for instance, they may be replaced with an algorithm to calculate simpler endgames on the fly.
Why is Rybka 3's engine smaller than rybka 2's?
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Rybka 2.2n2's engine is 7.5 mbs, and rybka 3's engines are all about 2.8 mbs.
I wasn't sure I had the right engines, so I pitted them against each other, and sure enough, Rybka 3 won all but 3 out of 14 games, and two of those were draws. how is that possible?