RHEL tends to be more security focused than Ubuntu, as in SELinux now being standard.  As such, their security patches are more frequent, and it's your company's choice as to how often and when to apply these.  They are both solid OS's.  

As far as VM's go, there is a necessary level of experiience required if using VMware.  It's easy to over subscribe and you never want to allow this to happen.  There are customers that use one VM per physical machine to avoid conflict.  It's all about your production needs.

It's really a horserace that depends on the application.  IRIS tends to favor higher clock speeds, which implies that Intel higher clock speed chips are better.  However, Intel makes a LOT of lower speed chips, so buyer beware.  AMD does a better job at hyperthreading, and the increased core count can really offset the somewhat lower clock speeds.  In an application like TrakCare, where there are many users, this is advantageous.  In Health Connect, the higher clock speeds may have an advantage.  As always, this is implementation dependent.  If in the cloud, you can test both with your application to determine which fits your needs the best.  AMD tends to have a slight price/performance advantage.