I think you guys are giving Command too hard a time. These guys are trying to balance the needs and demands of all of civilization while fighting for its very survival aganst odds they didn't know or expect.
First you have Bosch and ETAK. They had a plan, get what Bosch knew about ETAK. They had to keep him alive to do it. Mistake? No, it was a valid idea and remained so for quite some time. After all, the Shivans hadn't been seen for 32 years, who would Bosch use it on?
The Knossos blindsided them, I think. They didn't expect it, and when it showed they suddenly had three problems hit them at once:
1) Need Bosch's info on ETAK
2) Figure out how to use the Knossos to get back to Earth
3) Fight the Shivans.
Now, there is some arrogence in that last one. They fought and beat the Shivans the first time around, if by just the skin of their teeth, and now they had better weapons and the Colossus (which I disagree with being a mistake, it was a great tool for uniting the people of the GTVA and giving them a sense of security, how it was used wasn't great, but the ship itself was not a mistake). They could handle the Shivans.
Then there's Slaying Ravana, which only proved that the GTVA didn't know what it was getting in to. We see only the end of that battle, but I'm willing to bet the first phase was increadible. At the time, they may not have had the resources on hand to deal with it, and the bomber wing was their last chance of taking it out before it left the area. It's destruction was a moral boost and probably gave Command the idea that it needed to pour more resources into fighting the Shivans.
But then they could have shut down the Knossos, but they couldn't, and that's what started to hurt them. They had to leave it open for as long as possible, and when the Sathanas popped up, they did the only thing they could do: Run away. Pulled their whole fleet out of the nebula, destroyed the Knossos and set a defensive line in the first available area: Vega.
Now we get to Command starting to wise up as to what's going on. One super ship like this, and they're in trouble, another would be worse. Ships go back into he nebula looking for both Bosch and yet another Sathanas, which they probably figured was out there somewhere. The little black ops run through the second Knossos proved to be the right decision on the part of Command to order, and now they had to run.
Run very fast. There's not time to set up a defensive line closer than Vega, in fact I imagine the other side of both nodes were virtual fortresses. They were running an evacuation from a genocidal species, and there was no reasoning with them. Should the Colossus have stood it's ground? I don't know, one would think not, but we don't know why the commander of that ship chose to stay. Perhaps he knew more than he let on about the tactical situation, knowing that holding position (and the attention) would spare millions the wrath of that Sathanas. Maybe he was just a fool.
The point is, they did they're best against odds they didn't expect and that just got worse as time went on. Two things to consider here when thinking about it: A: Hinesight is always 20/20, and B: They're only human. Maybe that was the point.