I think the problem is that it feels really artificial and plastic - they clearly look to the likes of Buffy, Xena, Stargate, and maybe parts of TOS and Voyager when they're thinking about doing these genre-shift episodes, but the problem is that episodic TV of the past could do unusual episodes and have them work brilliantly because they'd already put in the groundwork of getting you familiar with the characters and world. They were a treat, the icing on a cake that consisted of many episodes of solid television. The spice, not the main dish.
SNW's spent so much time arsing around with meta stuff and gimmicks that there's nothing to build on.
I'm not one who has been dissatisfied with the "gimmick" episodes thus far -- not most of them, anyway -- but although I agree Season Three has proven to be surprisingly weak overall, I think SNW has advantages that other shows didn't have that have largely allowed it to make the alternating serious vs. "silly" episode structure work.
For one thing, SNW is a spinoff and doesn't bear the sole weight of establishing its characters and setting. The extent to which it utilizes prequel versions of previously familiar characters (Uhura and Spock, Chapel and Scotty, Kirk) and the extent to which it has a prior grounding in a popular Trek show does a lot of heavy lifting. It's gone a long way, I think, toward establishing goodwill among fans for a lighter-hearted format overall.
(I'll readily admit there are things that have disappointed me along the way: I initially thought Sam Kirk was going to be more present as a character who would obviate the inevitable Jim Kirk cameos, for instance, and I wish more had been done with him to this point. Still, I think the fact that SNW has so much familiar lore and atmosphere as ballast is a big part of why I have never felt cheated of "serious" SNW episodes by the format.)
The other advantage it has is that, while its experimental episodes certainly owe something to prior takes on those concepts, it is very unlike TOS in being able to choose and calibrate its silliness rather than simply being forced to resort to it due to limited resources. And the show's takes on things like the Musical Episode or its various excursions into Vulcan Farce (which I think we can say at this point it has made into its own subgenre) generally match or exceed the quality of prior whimsical outings in other shows.
At least, they did until the third season. In my opinion, S3's problem isn't its balance of serious and silly, but rather the degree to which both ends of the spectrum have been underwhelming. "What Is Starfleet?" is, I think, the first episode of SNW I've seen that I would have to call a full-on failure. The season's first three episodes are neither offensively bad nor particularly good. We've had one genuinely classic episode in "Through the Lens of Time," one really solid actioner in "The Sehlat Who Ate Its Tail," and a couple of lighter episodes -- including this one -- that have worked well despite their flaws (but even when they land for many of us as being fun and funny, they still do require us to squint at some fair-sized flaws indeed).
Across the board, I think there's a good case to be made that Season Three's batting average is just not a match for the high standards set by prior seasons, no matter what it's doing. On the other hand, when it has been good, it has been
really good. If the price of the misses is getting hits like Doug the Sexy Vulcan or the awesomely creepy Vezda, it's worth it.