I find several of the arguments laughable, because some people are attempting to theorycraft the projected future, without taking many facts into consideration.
A) A lot of people complain that MK is winning too many tournaments, but this IS in fact due to player skill at the top level. Proof? It is seriously likely that M2k would remain dominant if he played Snake. The same goes for Tyrant, and possibly Dojo. Pick the top players of any region. Imagine they mained Snake from the beginning of Brawl. They would still win, we would probably even consider Snake the best character, since his metagame would be the most developed.
Now, imagine all the top pros, including Ally, played MK. They would still win. Ally is a genius and a talented player and would win if he used MK instead of Snake, as well as other top pros such as Atomsk, and Neo who have amazing MKs that they simply choose not to use. I'm sure if players such as Anther, and possibly Lain played either Snake or MK, they would still dominate their regions. (Texans, you'll excuse me for not name dropping you, but you already have a top MK and Snake, so it'd be pretty redundant.)
B) Snake is no where near ban-able, and probably won't be the second best character in the game. In fact, it is entirely possible that Snake is not the second best character in the game now, simply that he has the most favorable MU versus MK, and perhaps that isn't even true. It's very hard to tell, considering that at the top level right now that actually does exist, Ally, Candy, Razer, Anti, and Fatal choose to play Snake over other characters. I feel like MK does protect Snake, but for other reasons than people suggest. I think since MK indeed does centralize the metagame, the MU vs Snake is WIDELY overlooked. Recently, I've been thinking that Marth is 50-50 with Snake. I go even with Ally in friendlies, and I believe Neo does as well. MikeHaze recently beat him in tourney. Havok beat DSF's Snake. I believe Snake is widely overrated due to the fact that most players simply have not dedicated themselves to exploiting Snake's extreme weaknesses, unlike the way we have tried relentless to exploit Metaknight's miniscule weaknesses. If MK gets banned, Snake might live on the top for a second or so, but as soon as he gets some real attention, in a metagame this developed (as opposed to when the game first came out) Snake will probably take a fall.
C) Ice Climbers are being stupidly ignored right now. They are probably top 4 characters in the game, and will be the most SCARY character by far if MK is banned. Now, some people say Snake wins. I'm not sure, I don't know the MU that well, and I highly doubt that the Snake vs. IC MU is highly developed. All I can really say with the lack of data is that IC are dominating two regions right now (Lain and Meep). Atomsk recently picked up IC, and he's ranked second on the PR with M2k gone, under ADHD, who SUCKS against IC, and has yet to fight Atomsk's IC in tournament. Despite any MUs, IC still have a broken gimmick. THIS is the character I'll be watching closely with MK gone, not Snake. Blizzard is really broken, and IC can overcome bad MUs through desynching, and is STILL an underdeveloped character. You're going to have a job explaining to me why a top IC can't get around an annoying strategy when there are two of them.
D) Bad characters will still be bad and average characters will still be average with MK gone. Please stop arguing this. The ONLY character I imagine taking a significant boost with MK gone is Luigi. Other characters on the tier list will shift naturally, because characters like Mario and Sheik are underrated, while characters like Zelda and D3 are over-rated (in my opinion of course)
E) Marth will be S-tier with MK gone. The entire Marth metagame does in fact focus on beating Metaknight. With him gone, Marth can then focus on Snake and D3. Neo has explained to me quite convincingly how DK loses to Marth. I personally am extremely talented at the vs. D3 match-up. Here's the best part: I'm very good at the vs. Snake match-up, and I've only RECENTLY started studying it. Since there are no Snakes in New Jersey except YES! who does not play in tournament, and Inui who does indeed play Snake but has always used MK vs. me, I never really had a significant reason to study the match-up. Now that I've learned it halfway, I'm doing fine against Snakes, probably because the MU is even. Considering Neo's style, I significantly doubt he has a problem with Snake. RoyR has notable victories over Snakes back in the day, and as I said, MikeHaze recently beat Ally. D3 is decreasing in popularity, but if the Marth plays correctly, similarly to vs. Snake, he can 0-80 the character through good edge-guarding and juggling. Marth needs to avoid getting grabbed, but with proper stage control and zoning, this isn't an issue. D3 has 0 safe pokes (Ftilt can be PSed and punished on reaction), Dashing in and doing anything including shielding loses to pivot grab.
That leaves R.O.B. as potentially the only viable Marth counter. I currently think R.O.B. counters Marth, but I am extremely inexperienced in the MU, and other Marth's say it's even, so we'll see. Marth will easily be S-tier, and potentially the best character in the game, taking wins over Falco, and Wario.
If MK gets banned, I'm looking at Marth, IC, and Snake in no particular order for top 3 in S-tier. Falco, Wario, and Diddy right after probably ending the A tier. Both D3 and Olimar are over-rated IMO. D3 has exploitable weaknesses and really ban MUs in Olimar, Falco, and IC. Olimar is misunderstood as a character, and gets ***** by high priority sex kicks which go through all of his low priority attacks. Next time you fight an Olimar in tourney, and feel like you don't know what to do, choose MARIO and keep throwing Nair at them, and jabbing if you hit their shield, and see what happens. I can beat low/mid level Olimars with Link. Of course, Olimar's metagame may develop, and they'll find good use in whistle and their transcendent UpB, but that's theory craft for a negligible future.
tl;dr
Metaknight is possibly broken at top level, but it's impossible to tell, because the best players are currently quite obviously winning off of player skill.