I'll be honest. The AI in Beyond Earth/CiV was the main reason I never bothered to even buy Rising Tides. There is no reason for a primarily single player game not to have a challenging AI. If it was too hard to code an AI given the hex/one unit per tile then they should never have used it as a primary game system. I'm frankly very disappointed they've never bothered to improve it.
This is the same [crap] product development choices that drove me completely away from the Total War Series.
1UPT is not the issue with the AI - the ranged unit system is. Most of the AI's bad decisions, from unit positioning to embarking within range of cities or enemy ranged units, boil down to being unable to appropriately factor in ranged units (and, later in the game, aircraft, as these operate in a similar way albeit with much longer ranges). Ranged units other than artillery should simply be dropped from the game - archers etc. would act like melee units with some kind of attack or defence bonus in much the same way as in Civ IV.
Civ V AIs are capable of dealing with aircraft to some degree - not as well as they should, but far better than BE that appears to have reverted to a pre-G&K form. Civ V AIs always build aircraft of their own and occasionally will respond to air aggression by setting interceptors; BE AIs never even seem to build aircraft. The Civ V AIs are also helped by the existence of anti-aircraft units, something that doesn't exist in Beyond Earth. Of course, aircraft don't use the 1UPT system, but they can be much more devastating in Civ V than in Civ IV.
Personally I wouldn't want to see the aircraft system change, since unlike every previous entry in the series Civ V does a very good job of showing warfare evolving over time (once artillery and later air power arrives, battles just play very differently) instead of just giving units stat upgrades - however the AI does need to be able to counter air power more effectively.
Warfare isn't the main failing of the AI in any event - the AIs are bad at it, but they're also typically bad strategically. Civ V's may be the best, in part because of the simplified tech tree relative to BE or Civ IV, but even so it will commonly get halfway to a spaceship, for instance, and then just stall. The military failings of the AI become a problem only when the AI has no other way to win.
In Civs I-IV, you generally lost to being wiped out by a hostile AI, or you won, since the AIs couldn't achieve any of the other victory conditions reliably (save in Civ IV diplomatic victory, since that was basically a subtype of domination). In Civ V the AI could compete and win non-military victories more consistently, so unless you yourself were going for domination its relative weakness in warfare was less important. BE's back to the bad old pre-expansion Civ V model where the game both can't handle 1UPT as well as Civ V's later incarnations and can't achieve non-military victories - in part because most of them have affinity thresholds the AI is apparently incapable of reaching before the player.