> Not to question the comptence of the varisys guys, but I guess ASUS or Dell are just
> more professional on designing hardware - they are just more experienced.

As said, Varisys are certainly not to blame for the design compromises made for the Cyrus/X5000. If anyone is to blame, then it's Freescale/NXP for the limited and incompatible SerDes configs provided in their SoCs, and maybe also A-Eon for commissioning a common board for two sub-100% compatible SoCs and requesting the given number and type of expansion slots at the same time.
I doubt that, given these premises, ASUS or Dell would have provided a better solution to this specific task.

> if one board performes poor [...]

AFAIK, the reason for the poor memory performance of Cyrus/X5000 (clearly contradicting the specs of the memory controller) has not been determined yet. We just know it's not the OS as it's equally poor on Linux, OS4 and MorphOS. This leaves the SoC (memory controller), the board design or the U-Boot firmware as contemplable culprits.