Look, I loved STXI even with it's flaws, but we're talking about a movie whose plot literally wouldn't happen if a) Admiral Marcus and Section 31 were competent enough to put a bomb in Khan's body or b) Khan simply beamed himself on to the Vengeance's bridge, killed everyone there, vented the ship's atmosphere, and taken it to Earth to get his vengeance.
These are horrifically obvious options that are being missed, not subtle points that require much analysis and thought to find.
And WOK was a movie that wouldn't have happened had Chekov of Terrell stopped for directions. Or, you know, counted to six and got stuck on five.
I mean seriously are people really going to say that whatever plot holes are in STID are worse then an inability to count to f@#king six?
1) We have to assume that there is no official record of Kirk exiling Khan. Ignoring the logs and flight records made during Space Seed, and Kirk having to explain where a member of his crew went too. As well as shutting up everyone on the ship about the fact that 72 super humans captured a frontline starship.
2) Chekov is a fucking idiot. Forgetting counting to six, how hard is it to say "Oh Ceti Alpha System? Yeah, Captain Kirk beamed down some guy named Khan--who will straight up kill us if he finds us--to a planet in this system, we better be on the look out"
3) Genesis cave: The tunnels were a staging area. Soooo...where's the transporter pads? The labs? Some way to beam up to the station or a ship. Starfleet really is an OSHA violation if they had engineers craving out tunnels with the only way out being to wait on someone on the station to beam 'em up. Hate for there to be an accident when the transporter operator went to take a piss.
TWOK hinges on everyone in Starfleet and especially the Enterprise crew being incompetent at their jobs.