IHMO, ISA does not matter because we are talking of a server and not an HPC machine.
What (I think) people really want is a server which can boot to full service in under a second, so that rebooting a server has the same consequences as loosing few TCP packets.
Because it is a 64 bits address, there is enough space to hardwire a lot of devices to a fixed physical address.
For instance, the first 64 ethernet interfaces start at a known physical address and occupy the same size; their presence is defined by a bit mask at a known address.
Same for the first 64 SATA disks, same for the first 64 PCIe and/or SRIO and/or Hyper Transport interfaces, same for the first 64 USB hosts...
You probably also want a quick access to extra memory which do not loose its content over reboot, both local to the processor and (another area) common to all processors - to store the state of remotely connected clients or the state of commited transactions in your database.
Because we are talking of a system-on-chip there is no need to probe for slow hardware which may or may not be there (at least for essential services to be provided), and drivers can be simple and efficient (statically compiled-in).
You may also want fast and powerfull DMAs for instance to store some ethernet frames (matching a header bitmask) to disk without processor intervention - or enable the ethernet subsystem to directly talk to a disk.
I do not think the ISA would be very important for such a server, but you may need a lot of activity/performance counters to identify bottlenecks.