What is the biggest difference between EMC Isilon and NetApp FAS Series?

Isilon is Scale-out storage, while NetApp is Active-Standby storage.

Regarding the performance issue based on the field engineer’s experience, Isilon is better than NetApp in case of a huge amount of io, while NetApp is better than Isilon in case of a medium amount of IO.

I think you need rewiew more than only performance or capacity, I have installed both machines, Netapp FASS have many options Hibrid or only objects, in Netapp Objects is StorageGrid where can obtain 720 TB in SG5760 but you can select SG6060 or SG5712 and Isilon is similar you have many options where could be ALL FLASH or SATA but Isilon is only NAS, and Isilon have many reference too, 8 reference F810 have 924 TB and up 250.000 I/Ops.

Actually I recommend one arquitecture where no focus only in one purpose, Scale up or Scale out all vendors have different alternatives and deppend the machine offer more I/O or Capacity, Midrange and High end, I don´t like Isilon because is only for NAS I dont like Hibrid or Unified Machines as FAS or VNX, I need to know which is the prupose for have a NAS because actually I can have a Storage for all protocols no only to CIFS and NFS and with prices cheaper than NAS, in conclusion I don´t like one Storage for NAS other for SAN other for Virtualization... Is better only one Storage where I can do it all, It reduce TCO.

My recommendation is to take a close look at our CS Concerto Scale-Out Cluster system.