In a nutshell you're proposing that lower level players will need enough commendations from higher level users to play with the "decorated veterans" of GoI.
You could name them that, or just "regulars"; there's 15 levels in this game, having a minimum requirement of 3 to enter a normal is relatively speaking nothing.
I don't feel the commendation system would be reliable to judge a new player. Giving someone a commendation at the end of a match has become the new 'gg' in GoI. This applies for veteran players as much as for beginners.
So commendations would not be given when such a player doesn't even deserve a gg, this is something that is good. If a player is working to keep up with the current playerbase and gets up to speed in the desired pace, they should have access to the regular pool. The idea is not designed to separate good players from bad players. It's to control the flow of newer players into the regular pool.
Conversely, a few mean spirited players could keep out deserving new players, at least in the short term. But that may be enough for a few players to get fed up and drop GoI entirely. Which leads to my next point, I'm afraid this system would encourage elitism.
Yes, again, the short term. They can be kept in the newbie pool for a little while longer before becoming regulars by automation. Secondly, the newbie pool needs some serious work as it currently puts in a whole lot of people that cannot even walk with people who wish to try to understand the game and wish to get better at it. That is what the second part of the plan was for. If players do not care about learning and playing the game proper, they can do so outside the confines of the regular and newbie pool. Alternatively, we can go to a newbie server and yell at these people until they stop playing.
Sure, in theory Muse could implement all sorts of reporting systems to go after players who give out commendations to everyone or those who conspire against new players. You also mention investigating players and processing 'appeals'. To me that just adds too much complexity to the game. And as far as Muse is concerned they probably already have enough on their plate, they don't want to be playing hall monitor.
Partially correct, yes it adds complexity for the Muse system should the majority of players decide to appeal the automated decision. But at least it gives Muse grounds to put people in or take people from that pool. That bit of monitoring can make a huge difference. Aside from that, I'm slightly hoping that such a pool will also make the players inside it realize that not playing together will not get anyone anywhere.
I'd approach GoI a bit like hockey: Call the penalties but let the players police themselves.
I'd be in favor of a kick system as well, but Muse said "HELL NO!! NEVER NEVER NEVER NEVER NEVER!!!" so this ends up being the next best thing.
Personally, I love the anarchic and open nature of this game. It really fits into the post-apocalyptic "Wild West" theme of Guns of Icarus. 
It used to work for lots of games, even dota. But when the trolls hit, they just hit hard.
