Because it's old. As an IT Consultant for for the last 15 years, my general rule of thumb is to look at upgrading a company's server every 3-5 years, depending on growth of the company and the performance of said server after 3-5 years. From a reliability standpoint, an aging server is more prone to failure and from a performance standpoint, a new server is faster and has newer technology. Most of my clients have always agreed and like to stay ahead of the curve.
In this case, we have a budget for a newer, faster server with more/faster storage, so we're not looking to recycle an old piece of hardware. While I agree that (for some smaller companies) taking a Mac Pro 2009 and loading it with Mavericks and some newer storage might work, that's not the direction we are looking for.
If, as has been said here, that a new Mac Pro won't give us any better performance than a new Mac Mini, then that extra $3000 can be better spent elsewhere, and that kind of advice I appreciate. Maybe with the savings one of the graphics Mac Pro's can be upgraded to a new Mac Pro!
I've run servers for clients out to 5 to 6 years. As long as parts were available, and a contract of some kind to provide at the least next-day coverage, we'd run them out older.
Given Apple's '3 years and done' hardware support, there is a big question on just getting parts. A 5 year old Mac Pro is going to be a relative headache to get fixed in a hurry if it's your main server. Even with a good backup, it's going to take time to get back up and running... I wish Apple would recognize that people running servers need better, and longer, support. Especially when you consider using an expensive Mac Pro for a server. 3 years isn't long enough, especially if they keep the thing(s) for longer than 3 years.
I've had clients that only upgrade servers every 4 to 5 years to fully depreciate the hardware. That's an issue on a server that can't get support past three.
At least with their old and killed server line, you could buy spares kits for them. Now? Hah... At least a Mac Mini server would be easier to change out...