This is what Graham Acre thinks of your arguments:
But, seriously, I know sending the Gundams back up into space without an escort is retarded as hell. I never said it wasn't. Don't blame that on the fact that the Ptolemaios needs to be recharged. That's like blaming the horse for the crappy horeshoes you bought.
to add yet another uselessness... the Ptolemaios doesn't go pick them up or anything like that, so...
And, finally, I know it's not really a 'flagship' in the sense of a fleet's flagship. But, in that it houses Sumeragi and Veda, it's at least a mobile command center, which, when coupled with other ships, would probably be called the flagship. Weapons aren't really an issue here.