The issue here is how Command has had this fame of being absolutely incompetent or lazy or dumb or annoyingly slow with regards to the events of FS2, but I would agree with NG that all the more careful analysis done here by many commenters actually support the exact opposite conclusion, that Command was cautiously optimistic in their endeavours, that they had made a proper risk analysis and decided correclty to porsue exploration with a small risk of a backlash, and that even when the Shivans proved themselves to be way out of proportion, Command proved to have substantial resources prepared and used them appropriately.
I've always agreed with that assessment, although I somewhat think that given we have access to a very minimal size of intel assets regarding these questions from GTVA, we are really just making informed guesses to their smartness and competence, so in the end it's somewhat subjective.