Absolutely. And a lot of what you write is perfectly true, especially in a RTS. Two players, each being the commander, fielding a fleet. One goes for quality Protos) the other for quantity (Zerg). In an RTS it's a good and proven concept, great fun. But the moment one player pilots the Protos carrier while the ther one plays a single Zergling, the second player very likely doesn't have much fun or success any more.
In the end, for everybody to have fun, every player should matter. Giving some players reduced value works against that. Especially when looking at EDs design. There's 1 vs 1. Which you could still say that it's your own decission to fly alone. But then there are wings. Limited to four players. It doesn't matter if it's four Haulers or four Corvettes. There is no balancing based on mass, ship price, combat value or anything.
The limit is "players". Four of them.
And that's a bit the shizophrenia of this games design. On one hand, they limit by player number. So every player counts. But only if the player also has a sufficiently big ship. Else he is basiclly worthless. I personally would really appreciate it, if FD would fix that. It would reduce (while probably not eliminating) a number of problems the game has. Balance, accessibility, new player retention, gameplay options, design of new content, etc. There's a number of things which could profit a lot from this. But as long as a sufficient number of people (among them apparently people at FD) believe that merely time invested (nicer word for "grind credits and engineers) should be the determining factor for power, this can not be resolved.
Depends. Before engineers came around, there were a number of people around who flew small ships. They still often were seen as at a small disadvantage, but not utterly outclassed. So such balance at some time was possible. The drawback of "at a disadvantage, but still viable" was overcome by "more fun to fly". Just getting back to this status would already reduce the problem a lot. Unfortunately with engineers around, i see no way to get there any more, without turning small ships into big ships in disguise.