I would strongly advise against this. While I'm a fan of ST:R, I don't see remaking FS1 or FS2 as going nearly as well, or a number of reasons.
1. Demand. Silent Threat was so bad it NEEDED a remake. By contrast, the mission quality of the retail campaigns (esp. FS2) is generally the benchmark of what makes a respectable user-made campaign (Derelict or Warzone, for example). It's only with Blue Planet and Vassago's Dirge that "Retail Quality" has been left in the dust, and unless you want to bring FS2 to War in Heaven's level, you'd basically by reinventing the wheel. Look at Bearbaiting, one of the most exciting missions in history, to counterbalance High Noon. High Noon is only boring if you had an epic run on Bearbaiting.
In terms of story: ya, there are glips, like the CB for Playing Judas. But like Battuta pointed out, the overall quality of the plot is powerful- that's why we're here today!
2. Scale: FS2, counting normal missions, SOC loops, and training missions, all of which would need to be rebuilt, is more than twice the length of the REMADE ST:R. And that's before increasing the mission count as part of the remake process. Take the number of years it took ST:R to be finished, multiply by three, and you're getting into Blackwater operations territory. Seriously, in terms of mission count, this could be one of the longest campaigns in history.
3. Significance. ST:R kept the "disruption" of canon to a minimum because not a lot of campaigns (good ones, at least) depended on ST to the point where they would conflict with ST:R. That's not the case with FS1 and FS2, where the very things people here want to change are often important questions in user-made campaigns, like the node inconsistencies and the lack of beams and flak on FS1-era Shivan ships (which is also critical for balance). Redoing the main campaigns would be an alteration to the very foundation of HLP and its work.
4. Symbolically, if we attempt to rewrite and rescript Volition's own core campaigns, we're basically severing the link with Volition- like a branch cutting the tree down. If we do this, we remove the very idea of Canon as something established by Volition that we must comply with to call our campaigns "compatible". We would be claiming the right, as a community, to rewrite FS canon as we saw fit. I think the refusal to do that was the reason HLP has refused to make a FreeSpace 3.
Maybe this is a good place to anounce that I'm working on a complete overhaul of FS1, STR and FS2 as one big package, with some added weapons and ships, new flight physics, changed loadout, improved AI, and all sorts of other "fixes"
I'm not sure how many people will take any real interest in such a thing, but it's being done
The overhaul as such is pretty much complete, and I'm starting to rework the missions as of now, so stay tuned
What?