Hi,
I just finished having my pool built and so I'm also new to this forum. In fact, this is the first posting I've done. I think you can save a decent chunk of money by not adding the spa as well as not having to heat it. I'm not saying don't purchase a heater for your pool, because you should. You simply don't have to pre-heat the spa for use when you want it (say 98º to 102º) and then have spill over of the heated water into the pool. Saving money by not putting a spa in isn't the reason why I chose to leave it out. As Matt says, even with the best spa combo with a pool, the spa does not perform like a hot tub, the latter having many, many more jets for relaxation. You could leave the spa out and save some money then if you find you're going to be in the house longer term, you could purchase a good hot tub. Use the money you save from not installing the spa to do some additional landscaping.
Regarding the shape of the pool, I definitely like the rectangular shape better and that's a personal preference. I'm also not really enamored with the Greek corners as I think it's a way to try and make a simple rectangle more attractive. Again personal preference. Have you considered the possibility of making the sun shelf longer and putting it on the long side of the pool closest to the house? In fact you could do a beach entry into the pool on the long side, keep the pool rectangular and curve the beach entry or sun shelf to add a bit more interest of a rectangular pool. Thought I'd throw out a couple of ideas to do perhaps in place of the spa.
I also recommend that if and when you would do a hot tub, to put it as close to the outside entrance door (if you have one) to your Master Bedroom. I have had hot tubs previously and also have a separate hot tub now, and I've found that type of placement to work extremely well.
Finally, I just wanted to comment on the concrete vs flagstone. I love the look of flagstone BUT you need to put sand between the stones (at least I think you would). I don't know what they use for a base for flagstone, but my travertine is on a base of crushed shells, then a layer of sand, then the travertine. What I've found is the base sand can wash out from underneath the travertine causing the stone to crack. I've already had the pool builder come back and replace a number of cracked stones. I don't think you'd have that issue with concrete. There are also a ton of options that you could consider for the concrete such as through coloring, staining, epoxy coating, stamping (as mentioned above), and more.
I'll leave you with this, the addition of a pool and the addition of an unground spa are the second and third worst investments you can make in a home based on ROI; installing an outdoor kitchen is the worst. Don't forget the cost to maintain the pool/spa, think about how much you'll use them. How much your energy bills will climb to heat the water. Your insurance is likely to go up and you likely will have to invest in a pool fence. In fact, some insurance carriers require it.
The paragraph above isn't meant to be a downer. I use my portable spa, almost every day, and I swim almost every day. I invest in both again in a heart beat. I just wanted to point out some things to think about because the house where you are now, doesn't seem like it's going to be your forever home. I hope what I provided at least gives you a thing or two to ponder before investing that kind of money in something where the ROI can be 0% to a max of ~25% depending on the area of the country where you live.
Good luck with your decision and Happy New Year!
Jay