Generally one could say yes to this question when one compares it with dedicated machines like the iMac or Mac mini.
If you compare with workstations primarily designed for Windows you will find the Mac Pro somewhat lacking. For the 2009 models I give you some facts:
HDD
Very well designed system if you stay with 3,5" drives. Takes up to 8 TB in SATA II HDDs and is capable of running them in several RAID modi.
SSD
Very poorly prepared for SSD as no doubling up of 3,5" drive slots for 2,5" drives is possible.
RAM
Inflexible due to specialized RAM specification and number of slots not suiting the internal controller structure.
CPUs
Very limited due to both hardware design aspects and firmware limitations. The octad sockets have no clamps which results to massive risk of socket damage in exchange operations. The original CPUs are without heat spreader which necessitates disabling the automatic coupling of electric heat sink connections. You basically have to destroy that mechanism and do it by hand. Traditionally Apple does not issue firmware upgrades when better CPUs become available. This often means that Mac Pro users cannot upgrade even if they have overcome the hardware limitations.
GPUs
Limited compatibility due to the firmware issue and also driver issues.