So why is this a (really) bad idea.
I think most companies I have worked for doing that. I am surely guilty of doing it myself.
I prefer the cluster view but still want to separate VMs. Folders won't work on VM level (unless of course you are in the VM view) so people tend to use Resource Pools.
In most environments it probably doesn't even matter. I worked in big corporates - they don't care if something is slow - they just throw more resources at the VM not fixing the underlying issue. Not realising that bloody resource pools are to blame. Plus they don't care who gets the higher amount of shares - they are all equally important.
Hosting companies - same principal .. Each customer has the same right to the resources, so who cares if one runs slower than the other, right ? Wrong ...
So here an example .. This environment (created Resources Pools in my lab just for the sake of demonstrating the issue as I cannot post screenshots of customer's environments).
In this environment, resource pools are really really bad .. because of the use of vCloud Director. ANd worse worse, because the vCloud Director pool is further down the chain.

So, here is why it is really bad ... two 'Main' Resource Pools.
-- Production
-- Development

So, you got vApps and Resource Pools in the top tree.
Here each vApp and Resource Pool get 16% shares of expandable resources - 16%
Let's go further down the production tree - as this is where vCloud Director sits.
-- Production
---- Clients
---- Own Stuff

Each Resource Pool getting 50% ... that is 50% of 16% ... that's 8% expandable resources !!
Let's go down further into the Clients pool - still chasing that vCloud Director pool
-- Production
---- Clients
Non-vCD
vCloud Director
Each Resource Pool getting again 50% ... that is 50% of 50% of 16% ... 4% expandable resources !!
And that is when you get errors like that in vCloud Director

So VMware, for the love of vGod, give us folders in the DC view