I came to think about the problem with having Resource Pools (or vApps) being siblings to VMs, and realized that this is exactly what installing vCops Manager does:
(inserting images doesn's seem to work today, so check this link: http://i.imgur.com/bzlbo.png )
I would suggest lowering the CPU and memory shares to make the vCops VMs get about the same or lower percentage of resources compared to the rest of the "normal" VMs.
In my case, I set it to "Low (2000)" for CPU and "Custom - 40960" for Memory. I guess you would have to customize this for each different environment depending on the circumstances and goals.
A good write-up on the background of this problem can be found at: http://vmtoday.com/2012/03/vmware-vsphere-resource-pools-resource-allocation-revisited/
vC Ops is very ressource hungry, reducing the number of resources might lead to missing data and inaccurate results.
Based on my experience it really needs the ressources based on the sizing guides in install / training material, going below that is not what I would suggest.
That's a good point. However, this prioritization only comes into play when the whole cluster is having too much demand compared to available resources, so I guess it comes down to whether one wants the production servers/applications or the vCops VMs getting most of the available resources in such a situation.
Of course, it might be nice to not be "administratively blind" when one suddenly gets such a resource problem, so being able to click around in vCops might be a wise prioritization choice.