Except most of the time, on the average ship, a single Engie COULD manage the important stuff, as long as someone was dedicated to serving as a secondary repair person. Lets use your "problem ships" as an example.
All ships are "problem" in encounter. There are no interest in maximum possible HPS, the repairing-bebuilding-cooldown balance is based on idea you need to be IN proper time ON proper place. That is why we have "responsibility" zones on all the ships, where parts are divided between engineers focus.
Pyramidian: It only ever needs one Engie anyway, as the Engie's entire job is sitting on the lower deck keeping the hull and engines working. The second engie is always stationed at the balloon anyway. This job can EASILY be managed by a Comm Officer, or even a Gunner. The ability to super-repair is NOT a necessity for this. Hell, the Comm Officer takes Mallet, the Gunner takes Spanner, and together they can maintain the balloon and guns, leaving the engines and hull to the actual Engineer.
Fisrt enemy with caffonade or flametrower (or incendiary carronade) will be your painful death. Because destroyed baloon is a HUGE HOLE for hull damage. As well, balloon is most vulnerable to fire, so that it must be chemspayed all the time. So in the situation of real combat your people will not be on guns, but on baloon.
Galleon: Really, the Galleon is a tricky ship even with 2 Engies, so it's a ship that may not want a Comm Officer. However, if one is used, it could be assigned to the lower deck as a Gunner Comm Officer, maintaining the weapons lower-deck engines. Meanwhile, the Pilot actually sets up to help repair the balloon in a pinch, and the actual Engie goes where needed, with the Hull being their primary focus. While two engies could maintain the ship as a whole easier, it's not absolutely necessary. This ship does require more coordination between all the members regardless though.
You have not even invented the new class, but already founf where is it unneccessary. 
Spire: A single Engie can actually maintain the entire Spire pretty easily if they know what they're doing, as long as they can keep the armor up. It's possible to hit the Hull with Mallet, drop down and hit the Balloon with Mallet, and get back to the Hull just as the cooldown from Mallet ends, and hit it again to start the loop over. That said, I'd put the Comm Officer on repair duty primarily on this ship, with their role being to repair destroyed parts rather than to keep things alive. Once the armor can be restored, the main Engie can easily use the parkour loop to restore the armor while maintaining the armor on the other part. Fixing broken engines and guns can be shared, with shooting happening whenever. Again, they don't need super-repair power, they just need to not spend 90% of their time on the guns. Even a Gunner could fulfill this role in the current game, if they didn't sit on the guns all the time. While they will obviously not be able to pull the trick the Engie can with Quick Repair then full Armor in a very short time, they can do basic repairs.
I really want to see you playing as engineer, because you seem not to be much realistic.
Basically, let the Engie deal with the Emergency Repairs, while the Comm Officer deals with routine maintainance, buffs, and information warfare. All of which it can do while doing said routine maintainance.
Everyone does emergency repairs. Even pilots. Lueosi participated in rebuilds hundreds of times.
Now, as to what you've said about Pilots. You seem to have this belief that a Pilot, the only person on the entire ship who can effectively fly the damn thing, would lose their role as Captain if the Comm Officer was made.
Good pilot is a leader with 8 hands, who manages setting crew, setting teammates crew, setting good enemy team on opposite side, talking with crews on match, talking with ally, deciding tactics, taking up conclusions, and well, for the last thing he moves the damn thing. Appearance of person who can be in charge for strategy will move a pilot to crew slot. And a lot of pilots will not like it, and decide to abandon the game.
I admit to not really playing Engies, but I have practiced in Practice Mode with them, actually testing out various Parkour things and trying to figure out how I would manage repairing the ship. I have personally managed the Spire trick on a heavily damaged Spire in Practice, so I know it's possible. If the armor gets broken it becomes much harder, but that's where the Comm Officer with Spanner or Wrench can help by covering repairs to destroyed components where possible, especially balloon or hull, leaving the Engie to actually heal the armor when it's back up, while keeping on the move so it can get to wherever they're needed. If this is feesable or not is something that needs to be tested, but it can be tested in game right now simply by taking 2 gunners and having one act as the Comm Officer would and seeing if it works like the theory says it should. Of course 2 Engies will be able to keep the ship in working condition EASIER, but the theory isn't that it will be AS GOOD, but GOOD ENOUGH. If of course it's proven to not be the case, then of course the concept has failed, and that's the end of it. Of course, the Comm Officer also has mostly tools that work on various components like the Engie, so they can end up moving around like the Engie would anyway. The role of the Engie making this circuit to maintain the Armor on Hull and Balloon could actually be swapped to the Comm Officer, leaving the Engie free to maintain everything else, but this obviously wouldn't work as well using a Gunner as a test.
That said, dispite your argument, the Comm Officer is STILL not going to kill Pilots. As has been said by others, the Pilot can only lead because they have only one job that doesn't require them to run around the ship like a chicken without a head that has tunnel vision. Comm Officers have to run around just like the other classes, or be on the guns. They COULD be a replacement Captain, but in that case they give up maneuverability as they would HAVE to be on the Pilot Wheel, thus also limiting what skills they can use to only ones that don't require them running to components. The Pilot will always be the better option for flying the ship, and thus being Captain, because they have no reason to ever go anywhere except for emergency repairs in the most DIRE of situations.
As for the balloon being on fire.... you do realize there are so many ways to deal with that it's not even funny? An engie stationed up there doesn't even need to chemspray it, the main engie could run up there to do that if its such a big deal. That said, the setup I was talking about is specifically designed to repair the balloon just as fast as an engie, but requiring 2 people. Yes, that means you stop shooting. But when the ship is dying, you tend to stop shooting ANYWAY because you can't hit targets as you're falling to your death. That said, in a "combat situation" only one gun ever needs to fire on the Pyramidion at a time. The Comm Officer with a Mallet makes sure the Balloon stays up while waiting for the gunner to take out the armor, then the Comm Officer switches to shooting while the Gunner moves to fix the balloon as soon as it finally breaks. The Main Engie could even just take a fire extinquisher and extinquish fires that way, rather than using chem spray. Only time I ever even need chem spray is if the enemy actually takes a flamethrower anyway.
As for the Galleon not needing a Comm Officer... of course not every ship needs all the classes, if they did then something is wrong. Ideally, it should be possible to take 2 Gunners and 1 Engie and still be considered viable in this game, but that's not the case right now. While a Comm Officer can offer some value, the Galleon is a pain to manage in general, so it's a situation where two engies can be more valuable than the tactical ability of a Comm Officer, no matter the situation. That's not a fault of the class, but a simple fact of the ship being that much harder to fly as a crew. While it's POSSIBLE to take a 1/1/1/1 team, it's not likely to be as effective on the Galleon as it would be on other ships, due simply to the problems you'd run into on the Galleon.
