Right, I've been wanting to talk about these two for a while now and I've been sitting on this essay for too long so I'll keep this simple and just answer the questions in the OP:
Misdreavus:
1) Is Misdreavus broken?
Maybe not broken but it is very powerful. It can run several sets and has amazing stats to back them up. The Nasty Plot set is an incredible sweeper, given that the opponents dark types and/or Fletchling is properly dealt with. Checking it is difficult due to it's great movepool and stats, but it is easily revenge killed by powerful dark types like Pawniard, as well as Fletchling. So Misdreavus can be considered broken by virtue of it's sweeping potential and great movepool being able to threaten the entire tier after one turn of easy set up. I was originally against banning it, but after considering it's I can see why Misdreavus can be considered banworthy.
2) Is Misdreavus making Little Cup not fun?
No, Misdreavus is powerful but it is not enough to make Little Cup not fun on its own. It is very powerful but not that limiting to the team building process as it still allows for player interaction. It is a powerful pokemon, but not really a degenerate one so it doesn't really make little cup not fun.
3) Is a combination of 1 and 2 deterring individuals from playing Little Cup?
I'll talk about this later, as my answer for this is the same with Fletchling.
Fletchling:
1) Is Fletchling broken?
It kind of is. It isn't so overpowered that it dominates the tier and is unstoppable, but at the same time it is powerful enough that it limits every team by forcing them to run a specific counter to it. It is very hard to check because of its priority allowing it to ignore speed in all but a few cases. As such Fletchling is a very centralizing pokemon. You either run one of it's specific hard counters or you get destroyed by it. Even among it's counters it is still very possible to play around them with it's moveset. For example, scarf Pawniard is usually a decent check to Fletchling but with overheat it can take one hit and kill in response. Because of how limiting it is I would say that Fletchling is broken to some degree.
2) Is Fletchling making Little Cup not fun?
Yes, it really kind of is. Because of not only how simple it is but because of how limiting it is to team building Fletchling does make Little Cup less fun. It is also difficult to play around it because of how its priority attacks limit what every pokemon can do against it therefore limiting player interaction.
3) Is a combination of 1 and 2 deterring individuals from playing Little Cup?
With both Fletchling and Misdreavus I would say no. They may be powerful and in some cases limiting, but they are not keeping people out of the tier. If any indevidual wanted to play Little Cup, then they would have already tried playing it and neither of the two suspects would really stop them from doing that. That being said Fletchling kind of is a problem in this regard. It limiting team building to the extent that it does can get one to become bored of Little Cup and stop playing it. So I wouldn't say that they're keeping people out of the tier, but they kind of are having it stagnate.
To summarize: Both suspects are very powerful and should be banned, but Fletchling more so as it existing is allowing team building to centralize around it and having the diversity of the metagame suffer as a result.