That "career midcarder" is a 3-time world champion who has beat nearly every top level star of his generation, with a pretty sterling win/loss record for the era.
As for not comparing in the "brutality stakes" he may not have had the flare for ultraviolence, but his accomplishments under the banner of extreme/hardcore rules speak for themselves. He held the ECW TV title for nearly two years, defending at a constant pace with every match being without rules. He was the last WWE hardcore champ, a title he won four times. He also had great results in matches with hardcore stips in the WWE beating a list of world champions that includes Guerrero, Booker, Jericho, Hardy, Christian, Dreamer, Big Show, and Orton amongst others aside from that Cena win. He also holds a Monster's Ball victory over Abyss while in TNA. So his resume doesn't put him as far off of Funk as you want to make it sound. And definitely shows him as a successful No DQ wrestler with vastly more pedigree than your typical "mid-carder".
So recognizing that even RVD needed outside interference to overcome Cena, despite having everything stacked in his favor, does make my point that it would be quite hard to think that Funk wouldn't have the same difficulties.
Trust me I'd like to side with Funk, but it just wouldn't be the right choice.
RVD's three title reigns:
Winning WWe title from Cena... held it for 3 weeks before getting dumped back to the midcard.
WWeCW title... created for RVD (ie, he didn't win it), held for 3 weeks.
TNA World Title... I'm a TNA fan but even I would struggle to endorse this reign considering it came at the height of TNA's delusions of grandeur... plus, what happened immediately after this 4 months reign (back to the midcard).
2 year ECW TV Title reign... so he was the holder of the third biggest companies midcard belt for 2 years
The last WWe Hardcore Champion... ... ... ...
Did he win it from Molly Holly?
The only name you've listed in RVD's big name hardcore defeats who is renowned for brutality is Abyss and he loses more Monster's Ball matches than he wins.
Comparing this to a 460 day NWA Title Reign (which means you were regarded as a big enough draw to go from territory to territory as the NWA's number one guy) is, frankly, laughable. Plus Funk was more brutal than ECW before there was an ECW. Funk was good enough in his prime to give Cena all he could handle in a straight match, throwing in that he can brutalise Cena until his (black) heart's content gives him the decided (and deciding) advantage.
It's a load of bullcrap to look at meaningless matches and count them in any of these arguments. We're talking about a winner take all tournament where one loss means you're out. Your back is against the wall in every match. The last time Funk was in one of those, it was in Japan and he beat lesser guys to get to the finals. There he met Mick Foley, someone who never held a title to that point. Foley won. John Cena isn't Mick Foley, he's much better. There's no way in a tournament like this that Cena is being booked to lose nor is John Cena the man going to let himself lose.
If we're talking about Hardcore Funk, he put over guys like Tommy Dreamer, Mick Foley, and others when they weren't stars. You don't think Cena who is THE star is going over?
Hold on, which argument are you putting forward here? That Funk will put Cena over or that Cena will win because it is a knockout tournament? One does not support the other - if this is to establish the best, then Funk sure as hell will not want to put someone over (who doesn't NEED put over) in a venue and a style that suits him better. Again Funk was 'Hardcore' before ECW existed so don't try and play the "he was really old before he knew how to hurt people" argument. Oh and Terry was a big enough star to be used to promote the NWA World Title across the territories when he was champion for 15 months!
So the stipulation favours Funk; the venue favours Funk; HISTORY favours Funk! Despite comments to the contrary, Cena doesn't always overcome insurmountable odds - he lost to RVD in this style of match and arena, he lost to CM Punk in this city due to his own stupidity and he lost to the Rock at WrestleMania due to his own stupidity.
If it walks like a duck, quacks like a duck and has feathers like a duck... chances are it's a duck. Everything about this match says Funk... so vote Funk!