Animations for the Reapers' "arms" should be possible. I haven't looked into what kinds of animations are available and what hooks are necessary, but AFAIK the animation code is more robust than it used to be. A simple idle animation with the tentacles swaying back and forth slowly should be enough for immersion purposes, with more pronounced effects when a powerful beam is charging (do Reapers have "main beams"? ME1 and ME3 are inconsistent, ME1 using the tentacles as emitters and ME3 having that center thingy).
As far as battles themselves go, they were never planned and choreographed beyond "two sides firing at each other" because it wasn't necessary for ME, they were just setpieces. I imagine a ME mod for FS would play very much like FS: swarms of fast fighters, slow capships that are mostly backdrops and/or mission objectives, fighters being a deciding factor in engagements but only in large numbers.
-Norbert-: The ME codex entires are good about being realistic and relatively hard SF, but that's because they don't have to be balanced for gameplay, fun, or narrative. Actual missions in a FS mod would have to be modelled after the cutscenes more than the codex entries.
And, of course, the horrible ME3 reaper beam sound would have to go. It's ridiculous. Its existence in ME3 was worse than the original ME3 ending.