Whoa, my topic got moved and all of a sudden I have a flurry of responses! Thanks Goober! And thanks everybody else for the support!

Anyway, you have an interesting idea Culando, but I don't want to change FS2 any, though, just the interim between FS1 and FS2, which brings me to my next idea that I would like to discuss.
First things first, please post any glitches or PM me if you have any problems. The only mission that I rescripted was Clash of the Titans, and that was only because the Tantalus was too far away and wasn't oriented to where its beams would pose a threat to the Bastion, and I scripted the launch of the first bomber wing to 30 seconds after the player destroys one of its beams to give the player time to do what needs to be done. Other than that, the game's the same except the Shivans have beams and aren't afraid to use them. You might also notice that standard lasers are a bit faster, but their fire and damage rate is the same.
Okay, I'm sort of mulling over what direction to take next. As this mod sort of met with mixed acceptance, I'm going over possibilities in my mind. I could conitinue with this, rescript Silent Threat, and then continue on to the campaign where flak guns and how they are acquired by the Shivans is brought about. Or, I could scrap this mod in its current iteration, to allow for greater community acceptance.
This was my thought, instead of changing FS1, leave FS1 alone, in its retail version, and instead add to the events shortly following Silent Threat to create continuity. This is how I was thinking about going about it:
Some months after the events of Silent Threat, a Terran and Vasudan project creates beam technology using captured GTI engineering documents and equipment. They also recreate the GTI's efforts at ship-shielding and manage to shield an Orion destroyer and arm it with the new beam weapons. It turns out that the beams from the Lucifer and the Hades used a rare focusing crystal, the size of a small asteroid. Neither the Terrans or Vasudans could find equivalent crystal and intead used replacement ones that, although work similarly, are not as effective, so these new beams are not as powerful as the Lucy's or the Hades', and they glow green instead of red or orange-red because of it. This destroyer would house no fighters since the generator powering the shield system was designed to fit into the hangar bay. You are assigned to another destroyer that is part of this experimental destroyer's task force.
Command has decided to deploy this new shielded beam-equipped Destroyer against the remnant Shivan forces. Preliminary tests go off without a hitch. The Orion is impervious to enemy fire and all, and its beam weapons allow for quick kills. Meanwhile, intelligence spots a Shivan repair depot in some system or another. Multiple Shivan vessals are spotted in the vicinity, including a Demon. This destroyer is dispatched to destroy the depot along with all enemy capital ships and your wing is deployed to assist. At the start of the mission, things immediately take a strange turn. All the Shivan warships flee from this destroyer except the Demon, which turns to intercept. This is odd because ever since this Orion was first deployed, Shivans have been avoiding it like the plague. Suddenly, the reason for the Demon's audacity reveals itself, as it opens fire with its own beam cannons.
Mass chaos ensues as it quickly becomes apparant that the destroyer's shielding system, which was thought to be impervious to all known weapons, is completely being bypassed by the Demon's beams. The Demon's beams cause a reactor overload on the Orion, and it becomes unable to return fire in kind, and it becomes up to the player to save the day. Your wing is ordered to take out the Demon's beams, but you run into trouble as the Shivans demonstrate their new weapon, the anti-fighter beam. Because of it, many of your wing refuse orders to attack the Demon, fearing this new weapon.
After the mission, the TV forces work on building their own anti-fighter beams, while simultaneously deploying thier new weapon, the flak gun, created by Vasudan engineers who acquired a taste for "ancient" human history. (They got the idea for the flak gun by watching old WWII archival footage.) The TV forces abandon future plans to shield capital ships, since shields are useless against beams, and instead focus on creating better weaponry. There are many other aspects to this campaign, but it ends with the final defeat of the Shivans, and the dissolution of the GTA that transitions into the Reconstruction period.
Tell me what you guys think of this idea as an "alternative" to my current mod. The pros is that because it doesn't change retail FS1, it might have more community support. The cons is that it supports the "Shivans didn't use beam tech in FS1 because they didn't need it/were being good sports" theory that I'm not a big fan of.