I really value stacking in Sins, so I was a bit disappointed when I discovered how unintelligently the game handles stacked units.
When you have selected a stacked group of units, you will only have access to the "leader's" antimatter instead of seeing a collective pool. To make matters worse, it'll by definition be this unit that executes any orders to use abilities, irregardless of his relative location to the target and his fellow ships' locations. This adds an unnecessary element of luck to the game. While this is also a relevant issue for any non-stacked selection of ships, it is somewhat alleviated under these circumstances by the fact that you can cycle between units between and their abilities with Tab. This isn't possible with stacked units (unless you've selected two stacks of units, and that's really isn't adequate).
I won't get into semantics about whether or not the issues at hand are bugs or if I'm requesting new features, but there's no doubt in my mind that these issues needs to be fixed, since circumventing the empire three and microing units manually in large scale battles quite simply isn't adequate.