It's really very difficult to answer some of your questions without a few more specifics and an understanding of your personal preferences. But here's my best shot without that information.
Gas and heat pump technology haven't really changed much other than gas have gotten a little more efficient but not so much that they've closed the gap much for operating cost on a $/BTU basis. Gas is about twice heat pump on this basis. Heat pumps have much lower operating cost but they heat more slowly and cost more up front to purchase. Typical costs I've seen HP are about half the operating cost of gas heaters per unit of heat. Problem for a large pool is that heat pumps max out at about 130,000 BTU/Hr. Gas heaters max out at about 400,000 BTU/Hr. Heat pumps are much more expensive to purchase on a BTU basis. For example a 130,000 BTU/Hr heat pump is about $4000. A gas heater that's 400,000 BTU/Hr is typically $3000 (this is equipment cost not including installation). Also, heat pumps lose some of their efficiency advantage as air temp drops.
So what's optimal for you depends on how long you want your season to run, what pool temp you require, and the cost of electricity Vs gas in your area. It would appear to me your original design was optimized for a fairly short swimming season for the pool and a longer season for the spa. But that's just a guess on my part. If you purchase a 400,000 BTU gas heater and plumb it to run for both the pool and the spa it will definitely raise your pool temp quicker and extend your season but it will cost a lot more to operate because operating cost for a pool pump on a $/BTU basis is about twice as much for gas heat as heat pump. Also, your gas heater may have additional cost for the increased meter size and gas delivery line. You need to check your meter size to determine these costs.
As to control issues, there really aren't any. You can control any brand heater with any brand of automation. At the moment I believe Pentair offers the best automation capability but I don't really think its advantages are leveraging for control of heaters.
If it were me, I'd check the cost of upgrading your gas supply to accommodate a 400,000 Btu/hr heater. If this cost is low, I'd upgrade to a 400,000 BTU gas heater and keep the heat pump. If the upgrade cost to the gas system is very high I'd probably go with the maximum size gas heater you can without the gas line improvements, probably at least 250,000 BTU and keep the heat pump. You'd be able to extend your heating season and keep the pool comfortable much of the time with the heat pump after the gas heater gets you to temperature. Your gas heater would also heat the spa very quickly year round in very short order and maybe the heat pump could heat it some of the time at a much lower cost. But this is driven by the fact that we swim a lot year round and want both available. Hybrid systems have always seemed to make sense to me for a large pool or colder climates with a shortened season but I don't see many of them. Perhaps due to the up front installation costs.
Please keep in mind everything I've presented here is based on typical costs. Electric costs vary by about 3x across the country and delivered gas costs vary as well. This can dramatically change the conclusions you would draw.
I hope this is helpful.
Chris