* Are there any areas in Middleburg such as subdivisions that you recommend or avoid?
I recommend the newer subdivisions such as the Retreat or Ravines Hill, or a gated community like the Ravines (not to be confused with Ravines Hill). Those areas aren't prone to flooding when tropical storms (or a couple of weeks straight of rain, like we had this summer) hit, like some neighborhoods on Black Creek are.
* Are there any areas that are not zoned or have fewer zoning restrictions? I'm thinking of building my own home.
Not sure. Check with Clay County and find out.
* What is the commute like from Middleburg to OP and closer to downtown Jax?
Middleburg to OP is a short commute, straight shot up Blanding Blvd. Yes, traffic on Blanding can be a real beast, but if you're only going to OP, it's not bad at all. Maybe 10 - 20 minutes, depending on which part of Middleburg you live in.
Middleburg to downtown Jax is another story. It's probably a good 35+ miles one way, and Blanding-to-I295 will likely be your best bet...and it gets to be a bear at rush hour. If you leave early enough, it's not bad.
* Are there any noise or traffic issues from Camp Blanding. Exactly what is Camp Blanding used for?
I don't live close enough to Camp Blanding, so I can't answer that. It's used as a training facility for the FL Army and Air National Guard units. There aren't any air fields out there for planes or helicopters (not that I know of), so I don't think noise will be an issue. Traffic isn't normally an issue, either, based on its quasi-remote location.
* I'm used to the flats fishing in St Pete and Tampa area. Does Jax have the same type of flats fishing. I'm now living in Raleigh and visited Wilmington a couple of times. They have no flats fishing.
Kinda sorta not really. There are places in the Intracoastal Waterway to fish when it's high tide that resembles flats fishing, in that you need a skiff or small boat to get up in the spartina grass to get tailing reds. There are TONS and TONS of fishing opportunities here in the Jax area, and if you move here, I'd love to show you a number of spots...your boat, of course!
* Finally, are there other areas beside Middleburg that is more of a rural, small town kind of place in the Jax area?
In Clay County, you have Green Cove Springs and Keystone Heights. The MAIN downfall to Keystone Heights is that it is even farther away from OP and Jax than Middleburg is...by about an extra 25 miles! Green Cove Springs is very similar to Middleburg in terms of being rural with some newer neighborhoods. I've lived in both, and have no complaints with either.
In Nassau County, you might want to check out Callahan. Callahan might be closer to downtown Jax than Middleburg is. It's not as close to OP as Mbg is, though.