I'll answer your comments specifically.
Criticisms
1 the Hecate was a poor replacement for the Orion as the pinacle warship with it's anti capital armament being unable to effectively engage corvettes and larger directly
Actually I believe Volition didn't put much emphasais on Hecate firepower since it never actually engaged a worthwile opponent. I've previously said that the only time true Hecate firepower was demonstrated was when the Aquitaine engaged the Tiamat and Abaddon (Moloch corvettes), but they're just corvettes. I would've wanted it to prove its worth by engaging an Orion destroyer, comparable in size yet supposedly "less heavily-armed" than the Hecate. On that, I recommend improving the Orion by extending its anti-fighter armament, then you have a perfect destroyer that can resist flanking techniques, unlike the Hattie (which, like the Ravana, only really focuses firepower on her starboard arc).
2 The Deimos while a valuable fleet asset and made for a more effective line support ship than any cruiser was to light to tacke heavy destroyers without signifficant fighter/bomber support
Frankly, I think the corvette is an excellent design. It can handle multiple cruisers whilst not taking too much punishment (considering it has 2.5 times the armor of some of the heaviest GTVA cruisers around), and can bring in a motherfrakkingly devastating anti-fighter/bomber firepower. Also, based on FreeSpace tactics, I think the ultimate destroyer-killers are either bombers or the Colossus. The GTVA fondly brings in a much bigger ship than their target, such as when they deployed the Psamtik to handle 2 NTF cruisers, or the Colly to handle the Repulse.
3 The fleet structure at the time of the Capella incident was split with the Terrans usinf fleets and the Vasudans using Battle groups, this needs unifying
IMO seperating Terrans and Vasudans in different fleets is fine. It's quite hard for officers from different races to handle their respective fleet, primarily due to cultural differences. An Alliance is enough. Did the British, Americans, and Russians fight in mixed armies during the World Wars? Not usually.
4 The Shivan incursion exposed a worrying focus on the Lucifer which committed the Aliance to a fixed approach leaving them exposed to new Shivan tactics
I think it was the Lucifer that the GTA and PVE really feared during the Great War. I mean, it was INVINCIBLE. NOTHING could stop it in hyperspace during that time, perhaps even a massive amount of warships combined with several dozen wings of bombers. Plus, destroying the Lucy is the key to destabilizing any Shivan threat, since they get "disorganized" when their command ship dies. And now, with beam weaponry, the GTVA just needs a warship that surpasses it in size and strength - that's why the Colly was made.
5 The GTVA Command had a dissregard for the potential for shivan escalation in the nebula which exposed the alliance to shivan counter attack
I can agree with that. Perhaps they shoud've sent numerous scout wings to explore the nebula, though I believe this is just useless given the said size of the system (10-20 lightyears). Command wasn't aware that it was heavily infested with Shivans.
6 GTVA Security Council ignored warnings that the destruction of the Knossos might not collaps the nebula node
When was that ever announced? I don't recall of any.
7 GTVA command placed too much emphasis on the GTVA Colossus
Like I said, they built the Colossus to fend off Lucifer-class warships, which is the most effective way in weakening a Shivan incursion. Also many members argue that the 20-year Project Colossus also consisted of designing new, powerful weapons and technologies, which led to the making of a new fleet.
8 On a number of occasions GTVA command acted in the NTF's favor in order to persue objectives with questionable benefit
Quite true. One of my previous theories was that the GTVA actually WANTED Bosch to communicate to the Shivans, but hiding the info from the masses so the leaders won't get kicked out of their palaces for doing what they think is right.
Recommendations
1 The Orion class need to be maintained as a heavy destroyer untill a suitable replacement can be brought online
Personally I view the Orion and the Hatshepsut as the two top destroyers of the GTVA; while the Hattie can bring in a lethal amount of concentrated firepower, the Orion can handle a wider area of defense with its evenly-spread beams.
2 The GTVA needs to invest in a new destroyer class to replace the Orion in a heavy destroyer role
Like I said, the best plan would be to devise an Orion with better anti-fighter capabilities.
3 An intermediate class/classification between Corvette and Destroyer needs developing
We already have one. It's the NTF Iceni; faster than any warship ever constructed, and has the armament, fighterbay, and nearly all the hitpoints of a destroyer.

4 While effective in some situations the Sobek has been overshaddowed by the Deimos class and a companion/replacement design with more emphasis on anti capital firepower should be considered
I've never really done a keen observation on exactly how deadly against capitals the firepower of the Sobek is, but I can say it probably has enough.
5 The GTVA Armada should have a unified fleet structure with the largest sub division being fleets and battle groups being used for sub divisions of fleets
We never really know the exact classification on ship groupings throughout the FreeSpace series.
6 A more flexable solution to massive shivan warships should be divised, the second incursion proves that we are a long way from going toe to toe with the shivans
With 80 Juggernauts plus the great possibility of a massive complement of a probable several hundred destroyers, thousands of corvettes, and tens of thousands of cruisers and probably over a million fighters and bombers, I doubt the GTVA will be able to scracth the paint on the Shivan War Machine. They just can't do it. They don't have the resources and fleet assets to handle such a powerful foe. Even with great tactics the Shivans are just TOO MANY.
7 Beam cannon research should be more heavily invested in
I don't think we have any reference pointing to just how much effort the GTVA did in the development of beam weaponry. The Shivans seem to be able to secretly adopt whatever the technology of their adversary is, and more; how did the Shivans suddenly gain better beams in every warship, and flak guns?
8 the creation of a planned "last resort" system to seal jump nodes should be created
Isn't the Bastion and Nereid enough for the job?
Hmm...now I begin to realize how interesting BP treated Freespace weaponry, and in the way they improved it.