The reason I ask these questions is primarily to well... make up a story
I've got what I need and will get back to you on that within the next couple of days. I'm off from work and well, needed a project that could be done in that timeframe (3D modeling? Not so much. Skyrim on the other hand, sure, but not as productive)
I've read your summary, but for a thirty - seventy minute thing, it's far too broad and you won't be able to get everything you need in as good as quality as you want. Consolidate the ideas, get detailed. Focus on an aspect, not the whole thing
Essentially, NTF conflict, Shivan conflict, HOL 2.0 conflict. Pick one of the three and roll with it. Don't try to incorporate all of them. Why? Too many different branches which you'll need to connect, explain, characters get out of hand, things get too complicated, you get frustrated, etc. Now, if you were to do three different thirty minute episodes, yes, that'd work... but not what should be three full length episodes in a single episode.
And if you were to do the NTF conflict, I wouldn't start it with an attack on an NTF outpost. Instead, I'd have it commence with an attack on a GTVA outpost. Afterall, it'd be far more engaging if the GTVA were to be caught off guard by a full fledged attack (and lose for once) starting the entire war between the two factions. This provides you with ample opportunity to give NTF some actual fighting credibility (as opposed to the chicken shoot they are) while introducing everything you need to about them. I'd steer clear of Bosch as one of the main characters as he's already been done, and you may want to base on something you've created. It makes it easier for you as you know exactly what this new fellows motivations are, as opposed to a character who hasn't been completely explained, and still has questions associated with him.
If you go with the Shivan conflict, have a single fleet battling them which parallels the main campaign of FS2, but isn't directly involved. Afterall, Alpha 1 wasn't at every single encounter. Just every single important one... This then becomes a story of the fleet, not the Shivans. You are right about them being mysterious, but not correct on the interactions part (It's "they're tearing our ships apart" by the way). How do I mean? Well, build on the mysterious. This is a fan creation, so don't pin yourself down on what they are, but what they're doing. Have a moment where this Shivan Warship jumps into a system only to hang out by a planet. When the GTVA come to battle it, instead of it doing what we all know and love, instead, anti-climax. It just... jumps out, no shots fired. You can then build on this mystery rather than the mystery of the Shivans
HOL 2.0 conflict: My opinion? Don't even bother. Trying to make it credible for Terran pilots to aid the extinction of their own race just won't happen. Vasudan's were more believable as they had the prophecies, and were at war with Terrans not a few weeks ago.