OK - lets start from the beginning - this is NOT a 'clip show' - 'Shades of Gray' from TNG IS a clip show - need I say anything more?? Let us once again review the circumstances behind this Masterpiece - and yes it IS a masterpiece:
About two or three shows into production of Season 1, Roddenberry, Solow, Justman and company realized that they were in BIG trouble on several fronts - shows were taking too long to shoot, post production on the shows shot already was dragging, Roddenberry was having trouble finding suitable scripts, and of course, the budget for the season was already starting to look scary. They already had slotted in WNMHGB to stretch things out schedule wise, so that was ONE season stretcher already. It was probably pretty much a consensus that there had to be SOME way to use that FIRST pilot in some way, even though the cast and look of the ship was totally different. One has to give Roddenberry HUGE credit for not only finding an original way to use The Cage, but making it one of the best shows EVER.
What makes The Menagerie so amazing is that Roddenberry basically wrote it very quickly - although not so quickly that they were able to make a VERY important decision. In one of the original drafts, they actually had Scotty find a solution to Spock's computer tampering, and they were able to regain control of the ship. But almost immediately realized that killed ANY of the tension involved. They then corrected that, and simply used the line about 'the fiction of a court martial, etc, etc....' Besides, to point out what should be obvious about the whole thing - the Talosians were in control of the situation the whole time! Scotty probably DID find the solution to the computer problem - except the Talosians would not it work--or rather make it SEEM it would not work!
Remember, that apparently Spock had briefed the Talosians about all of the factors involved, so that they COULD manipulate everybody involved.
And please, no griping about 'plot holes' - with beings like the Talosians, there would NO 'plot holes', as they had the situation well under control - literally! And besides that, even 'classic' drama by Shakespeare has 'plot holes' - its called creating dramatic tension folks.