One difference between Natural Gift shenanigans and Misdreavus's options is that Natural Gift can only be used once. If you mispredict and that berry gets used up, you are now facing a hard Fletchling counter. If you predict properly and fire off an Acrobatics, they're getting hit by a 55 base power attack. Even if you completely outplay your opponent and they switch their Fletchling counter in for it to get hit by Natural Gift, if they do manage to later heal this counter back up, you're still faced with a hard Fletchling counter. Overheat is another one of Fletchling's coverage options that is much more easily played around than Misdreavus's coverage options, although of course, this is to a much lesser extent.
Another difference is the sheer number of threats Misdreavus is able to beat with a single coverage move compared to Fletchling.
Let's just assume Fletchling is always running Swords Dance and Acrobatics, and Misdreavus is always running Nasty Plot and Shadow Ball (to maximize sweeping potential against a fairly healthy team).
If Misdreavus runs Hidden Power Fighting and Dazzling Gleam, it loses to Porygon, Stunky, and Lickitung.
If it runs Hidden Power Fighting and Substitute, it loses to Vullaby and Stunky.
If it runs Dazzling Gleam and Will-O-Wisp, it loses to Porygon, Houndour, and Lickitung.
Now let's take a look at Fletchling.
If it runs Overheat and U-Turn, it loses to Archen, Chinchou, Tirtouga, Porygon, Omanyte, Onix, Corphish, Shellder, and Elekid.
If it runs Overheat and a grass-type move, it loses to Archen, Porygon, Elekid, Aron, and Tyrunt. If this grass-type move is HP Grass, Drilbur and Corphish also take very little damage, and if it is a Liechi Berry, Slowpoke, Ponyta, Vullaby, Spritzee, Munchlax, and Snubbull will be able to check it due to the pitiful initial damage of Acrobatics.
If it runs Overheat and an Apicot berry, it loses to Archen, Tirtouga, Porygon, Spritzee, Munchlax, Vullaby, Slowpoke, Snubbull, Corphish, Shellder, and Onix.
If it runs HP grass and an Apicot berry, it loses to Archen, Porygon, Drilbur, Spritzee, Vullaby, Munchlax, Slowpoke, Snubull, Corphish, and Ferroseed.
If it runs HP grass and a Ganlon berry (other berries will fail to OHKO 76 HP/156 Def Berry Juice Archen after Stealth Rock, which is the first set on the Archen analysis), it loses to Chinchou, Porygon, Elekid, Aron, Corphish, Slowpoke, Ponyta, Spritzee, Munchlax, Snubbull, and Ferroseed.
If it runs Overheat and a Ganlon Berry, it loses to Chinchou, Tirtouga, Porygon, Elekid, Omanyte, Aron, Corphish, Slowpoke, Ponyta, Spritzee, Munchlax, and Snubbull.
I probably missed a few pokes in all of the lists, but my point is that possible checks to Fletchling are MUCH more common than possible checks to Misdreavus. Also worthy of note is that a perfect Misdreavus would want 6 moveslots; a perfect Fletchling would want 6 moveslots, but also 3 different items and no item at the same time.
The options to play around Fletchling are numerous; the options to play around Misdreavus are much less so.