I think when EVO allowed custom moves in their rule set Mii Fighters were more widely accepted because they could use customs.
Here are some of the problems I can think of that make Mii Fighters seem unfair, illegitimate, and illegal.
Banning customs: Mii's by default get to choose their custom moves. from the point of view of a non Mii main this seems unfair if Mii Fighters get to use customs and you don't. also from the point of view of a DLC character main Mii fighters customs seem extremely unfair because DLC characters don't have custom special moves.
They take too long to set up: unless everyone has their own 3DS handy to transfer you Mii's you will need to ether spend quite a bit of time setting your Mii up or be forced to use one of the default Mii fighters. Although this argument is kind of silly in small local tournaments, in big tournaments this is a legitimate issue. This won't seem fair to a Mii Fighter main that practices with a non default height and weight.
Over all the massive amount of customizations you can apply to Mii Fighters Physically and Visually scares away the community. We ether think the Mii fighters need to be simplified into specific custom sets's like at EVO or they need to be banned. That's the biggest issue affecting Mii fighters right now.
1. DLC
DLC characters don't have customs, but are also NOT vanilla characters.
They were sold to us without customs, although nintendo planed to make customs for DLC characters at a point and time.
Moreover, some people out there in the near future won't have all the DLC due to the price tag of each fighter stacking up. We have 4 DLC fighters worth about 31.95 USD in bundled packs, about 15.00 USD for each fighter separately (keep in mind that this not include wii&3ds packs). Therefore, Mii is easier to access than a DLC character because he is in the vanilla version of the game.
However, I see why it is unfair to you because you have no customs but customs are NOT an advantage. You can still play an awful game with hammer spin dash and lose to a non-customs player.
2. Set up ahead of time.
I for one also agree that major touraments could have a problem setting up miis, but that could be easily fixed. Taking notes from the swordfighter fourm on legality, simply set up beforehand on what mii you are going to bring to the touranment. TOs can easily set up an inbox for mii QR codes, and making sure beforehand that each QR code is scanned into the wii u ahead of time. So when the tourament starts, each mii is there and ready to use. If any mii is found inappropriate, it will result in a DQ on the spot.
3. Size
I understand why this scares many people away from mii entirely. I remember a post on smashboards which gave a fair amount of detail describing why Miis should be banned due to size which I will link at the bottom of this post. Size is nothing to worry about unless in extremes.
It's not the transfer time, it's the fact that you have to set up a 3DS system with all of those Mii sets, which does take a long time (source: I set up all of the EVO sets on my 3DS and transferred them to my Wii U) and then transfer them to your consoles. Setting up the sets alone takes a while, and then you have to spend a whole bunch of time transferring them to each of your consoles. It's not a big issue at small locals, but for big tournaments where you're working with 100+ setups (just throwing out a number) it's a huge pain. A long amount of time spent that isn't worth it. Same goes for creating different sized Miis. Say that it takes 2 minutes per console to set up the Miis (reasonable number). Multiply that by 100 consoles and it takes 3h 20m to create the Miis for all of your consoles. Multiply that by 150 consoles and it takes 5h to do so. This is disregarding the actual time to turn on each setup, etc., which would make this time in actuality a lot longer. It's a non-trivial amount of time and it only serves to benefit the...5 Mii mains showing up to your tournament. Now compare this to creating 9 default Mii sets on a 3DS and transferring them to each of your consoles. It's blatantly more easy logistically and allows Mii players to pick up their character and play without having to set them up on each individual console that they play on. Let's say, worst case scenario, there are a few setups without the Miis set up (like what happened with some setups for customs at EVO). Now you don't have to exit the game and create the Mii, then set it up on the system. I remember watching Blue doing this on stream a couple times at Smash Attack with Mii Gunner and it's pretty ridiculous how much time it takes to do so.
Other thing about a simple, set in stone list of sets: it allows players to create the Miis on their consoles and practice with their options aka knowing what they might run into. The other advantage to a blanket 1111/2222/3333, outside of simplicity and working out fine for Miis, is that it's no longer something we need to worry about. We don't have to change/add sets as the Mii metagame evolves, we don't have to worry about changing Mii sizes as the player understanding of them evolves. It's a list of sets that covers the metagame forever, theoretically, while allowing players to prepare for the specific sets that they're going to face and being an acceptable deal for Mii mains (at least to my knowledge/from the research I've done on this topic).
I see your point on time, but I have yet to explain my frustration when dealing with your arguments.
Not letting a character grow this the most underwhelming thing smash 4 has to offer, and sure the meta may hold stable ground during this transition into a mii-less environment free of potential outcomes. Speaking for the future, allowing a handful of mii fighters today, could possibly increase the number of possible mii mains tommorrow. As a result the meta develops, and each custom is known throughout each match up.
Also, your points on transfer are very deeply flawed. If your saying that it takes 2 minutes to transfer a mii, and then go off on a tangent to say that making nine default Mii's will help solve these times.
You don't have to set up your EVO mii on the spot, nor a homemade one. Just simply transfer it over on 3DS, setting it up on your 3DS BEFORE the event begins. In the case of a failed set up or even not having a set up at all, just DQ. If they fail to add the mii in for the system, simply scan a QR of that mii into the game using mii maker. If they take longer than 3 minutes to add their code, DQ.
I know the load times are killer when dealing with the transition between mii maker and smash, but that's the only way I can find an acceptable ruling.