Anyways, I've read all 18 pages of this and here's my thoughts:
Another Colossus? I would say YES. But any more than one is a waste of resources. Why one alone wouldn't be a waste of resources?
* Emotional Rallying Point - I'm sure there were minds in the GTVA Security Council that would have rather seen 12 Destroyers or whatever number during the construction of the first Colossus; towards the end of the 2nd Great War, I'm sure those minds would have seen the impressive kill record the Colossus put up, especially against a relatively unknown, new, outclassing-in-every-area Superjuggernaut. Not to mention, despite the loss of 30,000 strong, the lives they saved by merely being a target. Rear Admiral Koth, a notable and decorated NTF general, tried to ram the Colossus; if faced with one or two other destroyers, he might have ran or not pursued the course he did. This is a solitary example, but it nonetheless displays how the battlefield changes when such a construct occupies it. Because Koth chose to kamakazie instead of fleeing, who knows who else was saved from other hit-and-run attacks Koth would have participated in?
* Extensive Testing and Combat-Evaluation Period - You can objectively say that the 2nd Great War was the greatest Op-Eval period a combat ship can ever hope to go through. For being a first-generation "prototype", it destroyed 9 ships (varying from a NTF cruiser to a Shivan juggernaut) and was pivotal in many victories. For being designed to counteract the Lucifer, it outperformed itself in many areas. 2nd Generation refits and design modifications can only improve the excellent foundation the Colossus platform was built on.
* A Semblance of Security - Even if the public does or doesn't know how much of a supposed "logistical nightmare" the Colossus is, it's hard to NOT feel safe with a Colossus in orbit. The veterans of FS2 know better, as there are Sathanas' lurking systems away ready to shred it, if indeed that is their motive, so this isn't as "pro" of a Pro.
* Economic Boosters - Counting on 1 and 3, you could expect to see a boost in the economy of the system designated the construction point of the future juggernaut. With the need for secrecy gone and the construction needs of the Colossus released, its possible that many systems and companies would attempt to win the contract to build the Colossus, increasing the competition and economic plights of many of the systems that could be affected by the loss of Capella and many fleet resources. Once a bid is won, the winning system would most definitely see a large increase in trade and tourism, as intergalactic tourists would want to see the construction of this ship that was once secret. Losing systems, while not in possession of the contract, would not be poorly served by the increase in infrastructure and production ability. The GTVA could contract out the production of other ships, such as new Aeolus cruisers (Aeolus' would be a logical choice, since the reduction in force would necesitate an increase in multi-faceted ships), Deimos corvettes, and larger vessels. At the same time, those systems ramping up their capabilities would also probably need an expanded work force; Capellan refugees would probably be welcomed with open-arms! If I was a Capellan refugee, its no question I would be homesick, but a new planet that needs me, instead of shunning me, would be a very welcome sight.
* Cost - No question that after the collapse of Capella, the GTVA would go through an economic recession. To pay for the ship would be difficult, but not impossible. Note that in the loss of Capella, countless military assets were lost, but except for the 3rd Fleet HQ; all of the other Alliance civillian and trade installations (including those of Polaris, Regulus, and Sirius - I can say this because the Alliance was never sent to destroy any production or civillian installations. The closest thing ever to a civillian craft being destroyed was the NTT Sunder or the NTSC Hinton. It was never mentioned in the briefings (IIRC), and it also wouldn't make sense to if the GTVA was looking to retake those systems quickly. The GTVA could already out-produce the NTF by incredible margins, anyway.) would still be back in the other GTVA systems. The groundwork for a military is there, it's just there isn't as big a military.
* Logistics - Yeah, it would be tough. This ship isn't very manueverable, isn't as flexible, and certainly consolidates firepower that could be better served elsewhere with separate destroyers. Of course, you wouldn't make one Colossus, and that would be it. Other ships would unquestionably follow, negating this effect.
* The Need? - As Alpha 1 said in the end of FS1, "I'm told we can expect them again, but not in my lifetime." He was unequivocally right; they didn't come in his lifetime, but the fact that they might come again is enough motivation to do a lot. This massive warship would be completely ineffective against the pressing needs of anti-piracy and police action, but where's the short-term, long-term balance? It's my opinion that the pirates wouldn't be anywhere near as prevalent (outlying systems, such as in Derelict, would probably already have that problem, anyways) as in some of the non-canon, post-FS2 campaigns, but you can't just dismiss the pirates. On the other side of the same coin, if you spend all of your resources trying to eradicate the pirates, you will be woefully unprepared for the unpredictable Shivan advance.
EDIT: Removed Enif Station; mistakenly thought that was in Capella, it's really in Epsilon Pegasi.