I think it depends a lot on the underlying systems, and I can't say that I straight up prefer one over the other. For example, the action points in Fallout are based on Agility, Perks and Traits. They are the result of a specific character build. Characters with low action points are dependant on other stats to balance them out. Which was kind of a problem in the old Fallout games, as a high Agility was way too important for a good combat build. On top of that, there's much more intricate balance required for action point costs for everything. Simply figuring out how much potential damage two different weapons with different AP costs can do is a good example. It can lead to a much deeper system is much harder to balance.
The system in the old X-Com games wasn't great either. As most actions took a percentage of Time Units to perform, the amount of TU's available to a soldier mostly made a difference in how far they could run before taking a shot or throwing a grenade. And if their energy was too low, you couldn't make use of all the left-over TU's. You simply ended up sacking everyone who had too low stats.
In the new XCom's the actions aren't dependant on any stats. Everyone has two of them, and there's a system for how you can spend them. This makes balancing much easier, and it makes it easier to plan ahead. It can feel a bit simple at times, but especially in XCom 2 I think they've offered enough different things to do that it never feels like every turn is the same thing over and over.
So my answer would be: the one that fits the rest of the games systems best, and that provides the best balance.