After having lead a team in the freshmeat cup:
The buddy system is a great idea. Having an experienced player teach and guide other players massively helps them overcome certain prerequisites to fully integrate into comp TF2 and get them more experienced - like fermenting new yoghurt by putting in old yoghurt. Keeping them on medic is a no brainer too, since a medic maincaller is limited anyway, and if anything it helps enemy teams out by practicing killing experienced players with better jukes than the average open/low medic.
One thing I have a gripe with is logs weren't taken into consideration. The fact that a player could have 2k+ logs on tf2center/pugs but less than 10 open officials (or no open playoff+ experience) can participate with a casual guy that just wants to try out comp tf2 is crazy to me. I feel this cup should have catered to the bottom half of the table at the start of the knockout stages, because it gives the impression that these players should be as good as these 2k+ log / elo players, and I don't think them getting 5-0'd a ton helps their confidence a lot.
Also I think a team simply having an experienced buddy is a huge advantage, compared to a team full of freshmeat; each team should have been given someone atleast to guide them - how are freshmeat players supposed to even find mentors or any contacts if they haven't played comp at all
On a final note, I think there should be a pug discord solely for freshmeat players and experienced buddies to help them out. The cup was great but these guys should play together as a whole and getting integrated more into the pug scene can be huge for them. Just some food for thought