Well, I strapped a Mjolnir to a Leviathan and it still couldn't kill a Demon. Sure, it could take down Molochs and Rakshasas just fine, but LReds just kicks its ass.
I don't think strapping something twice as powerful would do much better, honestly.
Making a massive, fast, flying beam cannon could be done, but I'd say it would likely be at the cost of armor and anti-fighter armament. Think one big frontal turret (LRBGreen), six flak guns, and the armor of an Aeolus on something the size of a Deimos. It would be effective if escorted, but on its own it's just gonna get pwnt.
Orbital defense cannons would work - for all we know, they could actually exist. You never actually see something bombing a planet, so I don't know if they're really needed. It'd probably be a better idea to make stuff like GTI Acherons which can be dragged around to jump nodes by something common, like an Argo.
Tactical Theater-Range Missiles... Well, I'd guess they could make something like that, but what would they use for a warhead? Do recall that even the Helios is prohibitively expensive to produce and doesn't provide that much damage. There's probably a reason you only get to use helios once in the campaign, and only against the Sathanas. If the GTVA could afford to deply them en masse, I would believe that you would see them in use against the NTF... Also, even with a 20km range for TTRMs, beams beat it. Beams, at maximum, can fire 30 km. (For some reason, the targeting computers can only do 4km though...)
As for heavier bombers - the Ursa costs as much as a small moon (FS Reference bible). Every Helios it carries is prohibitively expensive to produce. if you want it to be faster than the Ursa AND better defended, it's probably going to be illogically expensive.
The Colossus had adequate heatsinks for its designed purpose: hunting down destroyers and superdestroyers. It takes six Orions attacking it simultaneously to bring it down, and it'll take down a good number of them too. The Colossus was never intended to go against juggernauts: the GTVA never saw a Sathanas before the Second Shivan Incursion.
Stealth on the Pegasus and Ptah relies on its small, slim profile and low power output combined with sensor masking and ECM. Heck, small stealth fighters were just being prototyped (after the Loki failed). Stealth assault fighters would come later, but not in time to help the SSI.
All in all, these would be some good post-Capella ideas, but for the time of the Second Shivan Incursion, I doubt any of these would be able to be implemented, aside from oribtal defense cannons...which are just upscaled sentry guns.
It's nice and all to go 'Oh, we'll use Weapon X. It's Very Effective', but you need to take into account canon situations and limitations if you want it to be believeable.