Well, there is no reason not to orientate your efforts on a game, that improved the gameplay of ufo.
Don't get me wrong, ufo was an incredible game for its time, and if this game gets completed exactly the way, ufo was, it is a great game. But this project is in a state it almost is completed the way ufo was, so it is really fair to look around to other games of this genre to see, what was done better there.
If it was on me to change one thing in ufo:ai the way, Jagged Alliance is working, I probably would change the movement system to the hybrid: realtime, when no enemy is around, turn-modus otherwise. This really helped keep action in flow during missions. But I know, this change would probably turn the whole game system arround and will not be implemented (at least not for a time).
But the Jagged Alliance games do have some things, whose integration is not illusorial in this game, like jumping over fences or opening crates. And yes, some of the gui-decisions of JA were quite good. Please, don't turn this game into a jagged alliance clone, no one is (or should be) wanting that. But please don't be closeminded towards ideas just because its origans are in JA.