On the whole I'm okay with the CGI effects; they're not great, but they do their job well enough and help sequences that weren't much to look at originally. Occasionally they're a bit disappointing, as in Doomsday Machine, and seeing the Enterprise twisting and turning like a fighter jet is always going to be wrong.
The one aspect of the new effects that does irritate me at times though is the way in which the new shots have clearly been pasted over
the original shots.
What I mean by that is - for example - say it's the end of the episode. We have a shot of Kirk standing on a planet looking pleased with himself, which then dissolves into a shot of the Enterprise orbiting the planet, along with triumphant music. Now, in the Remastered version, the shot of the Enterprise has
to appear earlier than it did in the original, in order to avoid the viewer spotting the original effects underneath during the fade from Kirk to the Enterprise. But that then means that we can get up to five seconds of the Enterprise before the 'look it's the Enterprise, hooray!' music comes in, and we may even still be able to hear sounds from the Kirk-on-the-planet shot while we're looking at the ship.
So basically what I'm saying is a CGI/extra effects shot has to appear earlier/disappear later than it did in the original, and this often throws the soundtrack off.
It was difficult to track down an actual screengrab to show what I mean, but there's a good example of when this process goes awry in A Taste of Armageddon, in the scene where Ambassador Fox beams down to Eminiar VII.
This is how the shot appeared in the original episode;
And this is how appears in the Remastered version. They've zoomed in substantially, and the pretty decent matte-painting has been given a bit of an (unnecessary, IMO) CGI makeover, adding a monotrain and extra people milling around in the background.
Staying with the Remastered version, watch what happens as we fade to the next scene;
Oops! During the dissolve the original shot is now visible alongside the new one, so we now have two cities and two sets of figures walking along.
Interestingly, the CGI'd shot completely disppears before we've even finished fading into the next scene, leaving the old one visible underneath.
9 times out of 10 they managed to avoid that problem by starting the fade earlier and trimming the start of the following shot, but occasionally baffling moments like that crept in...