As with almost anything enterprise, It's slow to change. We have several clients with tons of gear in our Datacenters that only can connect by PS/2, and by far the majority of their equipment only takes VGA. Most of the chipsets that do this have long been developed and are extremely cheap to manufacture. Like anything Enterprise, you pay for the privilege of it being made anytime this century.
With the whole economies of scale thing out of the way, there's other reasons too. VGA, for the largest part, is a unidirectional system. In VGA, aside from EDID, the VGA source just shoots the signal down the cable and hopes it gets there alright. DVI on the other hand is a bi-directional protocol. There must be a source, and sync, and they must be able to talk to each other. This is complicated by the fact that the KVM must act as a proxy server between the two DVI connections, acting as a sync and source target for each side of the connection. USB is the same way (though far simpler) in the fact that there has to be a USB host, and a USB device, and they communicate bi-directionally. PS/2's signal is bi-directional, but it's easily emulated as the only communication is clock start / stop controlled by pulling the clock signal low on the host. Once started, the KVM manages that session, and it's unidirectional.
And that's before you even get into DVI and USB's higher bandwidth compared to VGA / PS2.
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