Hi Ibreslin,
I actually like the design of the first pic you posted. However, doing a design like that would seem to cut swimming area. My with is already at a 11 ft putting the spa in the middle would cut the with maybe 3ft. Also I would like to keep the middle clear since that is were my cover patio is. The second pic would not me an option no space to put the space in that location in either side. I wish I could do something like the first picture, but due to the max with I can out i would not be able to push the spa far out of the cover patio enough.
Deep end by the spa is a nice feature, lets you plunge into cool water after soaking in the tub
Tell the builders you do not want the Nature II Fusion. It will add metals to your pool that can build up and be problematic over time. Personally I would skip the auto fill feature. They use the same technology as your toilet does (float valve) and are not that big a convenience. If you do go with an auto fill make sure they include a separate shut off valve in case it malfunctions. Ask for a waste line to be plumbed in before the cartridge filter. That way if you ever need to drain the pool or vacuum to waste you will have that option. Also ask for unions between each piece of equipment. It makes life much easier if you need to swap out or repair equipment in the future.
I like the look of the pool in the middle, but the one on the top looks like it will give you more swimable area. Think of how you plan to use the pool and the features you really like on pools you have visited. A tanning shelf with out chairs on it gives a wide area for younger kids to play in shallow water. How deep will your pool be? How long do you plan to stay in this house?