I have a basic idea for a few events and things I want in a campaign, and I plan to make it. Here are some ideas that I'm starting out with, and some principles I would like to follow, as well as general things that I have noticed:
- The mysteries left open at the end of FS2 demand answers, but am I really the one to give them? Is any player in a position to tell others what really happened? Sure, we can all theorize, and share our theories with fellow players, but telling them "This is the answer, everybody else is wrong" doesn't seem like something anyone but
should be able to do. Even they would need to gently disprove the people who theorized other things.
Any other general guidelines I should be aware of? I suppose some of these bulletted points could also serve as a set of rules for other people to follow, but I'm not going to suggest that. It would be too... presumptuous. And I'm not like that. Also, campaign and mission ideas are welcome. Technologies? See my thread in the General FreeSpace section (unless somebody moved it) if you have suggestions.
Wow. I wrote a lot.
Both retail campaigns (but not FS:ST really), and the two user campaigns I've played (Homesick and Derelict) start off with conflict between the Terrans and Vasudans, or the Terrans and pirates. I want to try starting with a Shivan vs. GTVA war, and introduce other elements.
Well, this is a great way to start off any campaign, so long as the action isn't dull and the player can feel involved in one way or another. Warzone started off with a Shivan vs. GTVA conflict and grew into the primary antagonist later on.
Character development is the reason I dislike Revenge: Final Conflict; it makes you have to put yourself in someone else's mind. I'm not great at that, and I'm not sure other people are either. Also, it makes it so different from FreeSpace. I don't want too much character development around the player. In Derelict it was acceptable, but it didn't seem that great to me. Around otehr characters, like admirals, scientists, and world leaders, character development might be a good thing. This is just my personal opinion.
Revenge was a little off at character development, I'll agree. Transcend, on the other hand, is terrific at putting the player in the place of the primary protagonist, but that may simply be because Ransom Arceihn is a god of storytelling. I personally like the third person character development like in Derelict, Sync, or Homesick; it's how I developed my characters in Rogue Intentions.
A variety of missions is necessary. You can't spend the entire first half of the game defending ships from pirates. Escort missions, attack missions, reconnaissance missions, story missions, and the occasional mission where things aren't what you'd expect from the briefing all need to be mixed in properly to create a good campaign.
They can be interesting if you do them differently enough. I'm not sure if I could word that any better, but essentially every mission involving action in Rogue Intentions revolves around defending two corvettes as they make their way through GTVA space, but each mission has something that makes it unique and different from the last. Transcend was essentially the same way, as was Homesick. A variety of missions is good for some types of campaigns, especially for those where the player is based on a destroyer and carrying out various military operations. I guess that may be why

switched the player through squadrons so often.
The Shivans are cool, but their motives are too unknown. They can't be left out of a campaign, really, but you can't have five Capella incidents without explaining why they're doing it. The same should apply to rebels, Vasudans, Terrans, and any other species you can come up with.
Shivans can be left out of a campaign if the story or timeline demands it, but most Second Great War-era campaigns involve the Shivans to some extent. Rogue Intentions and Transcend are two campaigns that come to mind immediately that don't involve Shivans. I agree with you on motives demanding explanations, though.
The main FS1 campaign ended with a conflict with the Shivans. So did the FS2 campaign (and so did Derelict). The only canonical exception to ending a campaign with the Shivans is FS:ST. Still, in Silent Threat, the GTD Hades incorporated Shivan technology into its turrets (other aspects as well?). Is it good to do it the same way, or should I try ending it with a conflict between the player's species (probably Terran, but possibly Vasudan, like in the Scroll of Atankharzim, very unlikely to be Shivan) and a species other than the Shivans? In FS1, the second-to-last mission threw in an HoL destroyer (the PVD Prophecy). Maybe a final clash between three power-players?
I've always enjoyed endings where different groups all participate to some extent, where two or more groups are allied against one ala the Starcraft and Brood War endings, or where there's multiple groups aiming at separate goals that all involve a similar area or object (Homesick, for example). I liked the ending in Homeworld: Cataclysm for this very reason.
The Hammer of Light is dead. They were destroyed in Operation Templar. I don't want to include them in my campaign, unless someone can come up with a darned good explanation of why I should. It doesn't make sense that any post-Capella campaign would include the HoL, unless, possibly, the destruction of Capella sparked some sort of resurgency in the Vasudans. It's possible, I suppose, but I don't want to make it the focus of my campaign.
Pathways actually focuses on a resurgence of the Hammer of Light, though the details will be left In Secretâ„¢ for now.

Any other general guidelines I should be aware of?
Whenever I develop a character, I actually follow Joseph Campbell's
Hero with a Thousand Faces guidelines as an outline. I can give you something more in-depth into this via PM if you're interested at all.
Some good points there. I agree with a lot of them, and it seems you've got a fair grasp on what and what not to put into a campaign. Should be interesting to see what everyone else has to say to this.