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That is a very good question and also a bit loaded without knowing anything about your needs\environment. Here is what I would say on the differences and where there would be advantages for one vs the other.
Empower is SaaS based. Aside from the Agents on endpoints, you have the need for the Sentinels which are lightweight just like our agent. No SQL, console install, etc to setup. Protect requires the on-premise console and a SQL DB and takes a whopping 30 minutes to install. So, almost a wash as it really is not that complex to get up and running.
Empower has more robust Asset capabilities, a web accessible UI, and a sexy sleek experience. Protect does not have the web accessibility and the UI may not be as appealing to look at. Empower slims down the UX to a very easy to use very simple to configure experience. Protect users are able to use the roll-up feature to roll their patch data up to Empower and take advantage of the visual appeal of Empower in representing the data and have access to your Protect data along side the Empower Asset and User data.
Empower has Mac OS X support.
Protect has the Agentless capabilities reducing Agent footprint in the DataCenter and especially in the Virtual Infrastructure. Empower requires an Agent.
Protect has a lot more depth of features in the Patch Assessment Templates\Agent Policies. Empower has the same product coverage, but you don't get as much depth of control for exceptions as you do in Protect. Deeper exceptions and more complex baselines are more critical on the server side than endpoints.
Protect has the Cloud Enabled Windows Agent enabling off-premise support very quickly and easily. Empower is SaaS based so it is always cloud enabled.
Protect has the Virtual integration giving us the ability to scan not only the Online VMs, but offline VMs and Templates. Protect can also take pre-deploy snapshots. Obviously more geared to server\datacenter.
Protect has a set of canned reports out of the box, Report Views for easy integration into SIEM or other reporting systems if you need to mine the data and pull it into another solution to centralize with other solutions.
Protect has more flexibility to schedule assessment, stage, execution, reboot as separate steps and can schedule one time tasks which is ideal in complex server environments where systems do not have a consistent maintenance window.
I could probably go on, but what I tell people is find the fit that is right for your needs. Empower is focused on the endpoint more than the datacenter and has some rich visual experience. Protect has a lot of strengths on the server side that few products on the market can come close to comparing with. Empower is a great compliment to Protect customers to bring the rich asset capabilities and the Mac OS X support, so many of our Protect customers are expanding into Empower for those reasons.