For the most part I really enjoy the remastered effect shots. But sometimes, sometimes I really want to throw my slipper at the screen in abject frustration.
Not because of the FX per se, but I sometimes get the feeling they were executed by a bunch of CGI artists on their own, with no general supervisor or animation director with actual film experience and knowledge.
For instance, DOOMSDAY MACHINE is my favorite of all TOS épisodes so any senseless alterations are going to jump out at me:
(1) I may be wrong but I'm pretty sure Star Trek as a show never used any cross-dissolves in its editing, for the most part hard cuts. But here at 1:07 the remastering uses a cross-dissolve to go from a bridge shot to a space shot for no reason (don't they know a cross-dissolve is to be used to indicate a passage of time?)
(2) at 18:12 not long after the Enterprise has first been attacked by the planet killer and separated from the Constellation, here they show the E flying straight towards the camera with no big gobbler behind it (this is a very wide shot BTW). Cut to inside the bridge with Spock saying they have outrun it (but not lost it). But at 18:40 we see the POV shot on the bridge main viewer at the planet killer looks like it is right BEHIND the Enterprise as it loses interest and turns around.
So where was it in the shot at 18:12? At least it should have been in the far distance behind the E.
(3) At 25:35 we see Kirk's POV on the Constellation auxiliary room's viewer of the Enterprise firing phasers at the planet killer. But right after that we cut to a bridge shot as Matt Decker yells out ''Fire''. Weren't they just doing that in the previous shot? The new FX made the Decker shot redundant. What they should have done was simply a shot as the Enterprise too dangerously approaches the machine, then cut to Decker.
(4) At 28:00 Sulu says ''we're being pulled inside'' as the Planet killer has locked a tractor beam on the Enterprise. But the FX shot seems to show the opposite as the Enterprise is basically fixed in space and instead the planet killer slowly pans into the scene. It can be argued this is a shot on the Enterprise as it is pulled towards the machine to make it more intimidating, but to me it looks more like the machine is approaching instead of the opposite the Enterprise is being pulled. The shot directly contradicts the intent of the line of dialogue.
(5) At 28:34 we have the classic bit where Kirk and Scott react gloriously to the Constellation's weak engines sputtering back to life and lurching forward to go fight its last battle (by the way, whatever happened to Washburn and the black guy during this?). I had always assumed that whole bit was to show that the Constellation was actually moving forward during this sequence.
However that is now contradicted at 29:08 as at the beginning it seems the Constellation goes from almost no forward momemtum to moving forward. This should have been a shot of the ship moving at continuous speed!
(6) At 30:23 the Enterprise is shown almost Inside the planet gobbler's maw only to be released and it starts to veer away. But man here the FX guys have the E too damn close to the maw, what about the brightness of its energies being almost blinding, as we see during the Matt Decker shuttle sequence later?
(7) Nothing to do with the effects

and I love the battle scene between Decker and the redshirt, but how is it a two-fisted blow to a man's back will render him unconscious?
(8) continuity problem: At 36:57 we see the Inside shot of the landing bay with the doors opening. I think at the end of the shot they finish opening completely but I'd need to see this on a much better screen. However at 37:08 we go through the door opening action again from the outside view. The remastering team should have had the doors only begin to open at the end of the first shot.