Most server boards a low profile these days. Mini-PCI is used because most 1U/2U rack servers are extremely slim. Since rack servers don't typically need any expansion cards added (things like RAID are often attached via NAS and most blade servers just crunch numbers anyways), the larger PCI-x slots are not used. However, at times IT professionals need both slim servers and the flexibility of at least 1 PCI slot. This is particularly true with blade like servers.
So the reason for mini-PCI slots is simple, flexibility without sacrificing space. 🙂
-mpjesse