As a former HD firmware engineer, I'll give you my opinion. Take it with a grain of salt, everyone and their dog has an opinion.
Thank for the wide range of suggestions! I never consider the possibility that even a RAID 1 could encounter problems.
I was told by an Apple Tech person to buy a decent enclosure and the drives separately. He implied that you don't know how good the drives are in the pre-loaded ones. I am not sure if there is any truth to this. Are G-Tech external drives any good?
In general I agree with this. Most external drives use the cheapest drives available. My understanding is G-Tech is a more premium product, and from what I've heard they use HGST He drives which are the best of the bunch. I haven't verified that myself though.
I am also wondering if I get a preloaded external drive and the hardware mechanism fails at some point, would I be able to transfer the drive to an enclosure?
Usually yes, they typically just include a standard SATA drive that can be removed from the enclosure. A few esoteric drive use USB direct to the drive, not sure how common that is though.
The other thought is to set the drives in OWC Mercury Elite unit to function independently instead of a RAID. One drive would be running Time Machine and the other drive would be Carbon Copy Cloner. Would that be a good strategy?
I don't see anything wrong with that strategy. I have seen enclosure fail, but typically you can just move the drives to a new enclosure.
Also, which would be a good hard drive investment...WD Black or Seagate Barracuda?
My recommendation would be to go with an HGST drive. WD acquired them specifically because they manufacturer the highest quality drives and were hoping that could rub off on their own product line. As for the WD product line.
WD Black - Quality drive, good performance. Use it for single drive application.
WD Blue - Cheaper drive, that focuses on cost/capacity. I won't buy one of these.
WB Green - Drive focused on energy efficiency and is what is used in most WD MyBook external drives. For a single drive backup drive this is a good choice.
WD Red - Drive targeted for NAS and RAIDs. I'd get this drive if you want a RAID config from WD product line.
Don't know as much about Seagate but I think the Barracuda is similar to the WD Black in their product portfolio.