Here is something to think about (if you haven't already).
From an OEM standpoint, recommending the use of the latest versions of equipment is usually no big deal. After all, they gotta make changes like this all the time and, after all, all the new features are pretty nice. Issues regarding incompatibilities between software and hardware are just part of the territory.
Now, if you are an end user who does little in terms of troubleshooting or modifications, this might still be a good choice. Typically you will need to call in your OEM to do any upgrades or modifications or you will call in a specialist.
If, however, you are an end user who is frequently tweaking your processes and going on-line with your PLCs for troubleshooting, I think you will probably want to fall back a step or two from the latest and greatest.
In this last scenario, your plant-floor-kinda-guys are typically the ones who need to get on-line to troubleshoot and/or modify a program. Now these guys do not need to be concerned about versions and lock-stepping. What they need is to get on their systems every time. Of course this is compounded significantly with every additional PLC in the plant. All it would take is one or two machines being different from the rest (and inaccessible) to create the impression that your system is all messed up.
From my perspective, it sounds like you would probably do well to stay away from the ControlLogix if you are planning an all-out plant upgrade. Because you seem to be looking for system standardization rather than additional features, I don't think the potential for future lock-stepping problems is worth the new features that ControlLogix offers.
I can't speak to the Omron system because I don't know anything about it. But if your OEMs are recommending it, just be sure they aren't recommending similar kinds of problems.
Steve