Every Star Trek show has those few episodes where you wonder what the fuck everybody was thinking. Even Deep Space 9 had shit like Profit and Lace, in one of the show's best seasons no less.
The difference is we didn't have Profit and Lace as the flagship installment of the franchise in absence of everything else.
I'm not talking about ill-conceived episodes, I'm talking about episodes that do head scratching things for no other reason than to move the plot along (much like the 2009 film did).
One of my absolute personal favorite TOS episodes is The Naked Time
. But in order for the Enterprise to be compromised we have to believe three absolutely insane things: 1) That during a critical orbit that the Engineering deck only has two officers on duty, 2) That Scott would be gullible enough to abandon engineering on the word of another officer with the only other engineer on duty, 3) That the engineering section has only one door and no way to override the locks.
It's an incredibly stupid set of events that have to happen to make the episode go, but the episode writing outside of that coupled with the acting make it one hell of an entertaining episode.
And you can count mountain sized plot-holes and other stupidities on about eighty percent of Trek episodes as a whole.