I have worked at two different companies who have two completely different setups so I will try and tell you the pros and cons of heading either direction.
Combining Disciplines Template
Pros:
Lower Overall File Size (Might Be Important for Small Companies)
No Need to Copy/ Monitor Equipment that needs power or circuitry.
1 template = 1 Set of Standards and Cleaner Drawings in my opinion.
Cons:
Electric vs. Mechanical may like to tailor their template in ways the other discipline may not expecially if you have an Architectural department. I come from a Mechanical side and we use different colors often to differenciate between systems among other uses as well, typically architecturally they use only black and then the printing in color option is not a problem for them, where we must change to change all to black lines as we print. This is not a huge step in the printing procedure just an example of the kind of problems you might run into when combining disciplines.
Separating Disciplines Template
Pros:
When a piece of equipment is changed or moved the Electrical Dept will have an alert when they open up their file if they are correctly "Copy/Monitoring" the element. Thus helping with coordination which is what Revit is all about!
Makes for a cleaner working environment in the each project. The Mech Designer is not constantly being bombarded with all of the electrical families throughout the project and vice versa.
Easy to Turn of Electrical/ Mech Model...Not Really Sure if that is a Pro or Con
Cons:
My biggest pet peive in seperating files are the titleblocks. In ACAD this was never really a problem because you were always sharing the same xref. Well if you seperate files in Revit you end up with two different titleblocks and since you are M&E you will probably be using an external titleblock family and since you can edit the family in one place and the changes will not update in the other unless someone is alerted you can end up sending out a set of drawings with slightly different TBs. I'm kind of particular and little things like that really bother me and I think it just makes your company look like they dont do any in house coordination. Title blocks are just one example while there are actually many items that may run into the same problem, examples being.....north arrows, tags, view titles, etc.
Im sure there are many important things Im leaving out but I hope this helps or at least gives you some ideas.
