The biggest problem that I had with the episode is this:
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I can't believe in a Starfleet General Order they would list "Half Vulcan Science Officer Spock" instead of just Science Officer Spock or Lieutenant Commander Spock. I know, I'm nitpicking.
Yeah, I had some fun with that odd phrasing in my review for that DS9 Risa episode. Just another example of early instalment weirdness.
Getting a good look at this, I now find that I'm dying to see or know the specs of a 3XY phagrin mass computer. Kind of a ridiculous sounding name (the operator must be a Vidiian displaying a particularly gruesome smile, or alternately makes me think of Dr. Sardonicus!!!!!

The Menagerie, Part 2
(*½)
And now the conclusion... where our heroes sit down and watch television for an hour. Just like in part 1, I'm going to focus on the new material in this episode, and there's not much. There's only 4 or 5 scenes, and they all more or less boil down to Spock saying “Wait, wait, the good bit is coming up soon, I promise.”
I strongly disliked the ending, where it was revealed that Commodore Mendez was Bruce Willis all along, because it doesn't make any sense and calls the nice tidy ending into question. It implies that the Talosians' illusion power can reach all the way to Starbase 11, so why didn't they just fake orders dispatching Pike to Talos? Why did Mendez vote to find Spock guilty if it was necessary to keep the trial going in order to distract Kirk? How do we know that the orders Kirk receives from Starbase 11 at the end of the episode are real and not just another illusion? Things would have made a lot more sense had Mendez been real, but I guess they wanted Kirk to be the one to make the ultimate decision at the end, and I feel that hurt the episode a great deal.
Maybe it's a little harsh to focus so much on that point considering it was a minor element of the episode as a whole. But when you strip out the material from The Cage, there's not much else to focus on.
Just so to all of the possible flimflammery cited above. What's always bothered me about the ending, is that Spock wheels his beloved old boss out to send down to the planet, and then about 10 seconds later, Kirk sees Pike making his way down to his old man cave. Now I realize that Kirk wasn't going to be shown staying in the briefing room for 5 minutes, whistling a tune, until the same thing is finally shown on the viewing screen, Why would he remain there at all after everyone has left? So, I guess the obvious answer is that the Talosians are doing him a favor while he's still in a position to see it, by previewing what will shortly happen, out of respect or gratitude perhaps in his helping to make the plan reach its desired goal, before he has the chance to walk out. Mighty nice of them and yet you still can't go there. It doesn't seem fair or warranted somehow.
This doesn't really apply since they were the last lines of dialogue in Part I, but I've always liked this exchange:
KIRK: Do you know what you're doing? Have you lost your mind?
SPOCK: Captain, Jim, please don't stop me. Don't let him stop me. It's your career and Captain Pike's life. You must see the rest of the transmission.
KIRK: Lock him up.
Especially, I like the touch of Spock's tilt of the head when referring to Mendez. I think it just seemed like a neat part of an unusually emotionally charged vision of him, that added to the gravitas I think the scene contains, helped also by that familiar, yet dramatic musical selection.