At the end of the novel, Gene concludes that what made Phineas different was his lack of resentment, lack of fear. Everyone, he claims, identifies an enemy in the world and pits themselves against it. Everyone that is, except for Phineas. Great, but the guy's dead. So it doesn't look like his viewpoint did him much good in the world, does it?
Let's backtrack a moment to Gene's final conversation with Finny, in the Infirmary before his surgery. Gene tells Finny that he wouldn't be any good in the war. He's too kind, too playful, too naïve to genuinely fight any real enemy. To Finny, it would just be sport, and sports are always good, and everyone always wins. But Gene isn't just talking about the war. (They never are, in this novel.) He's talking about the adult world from which the boys at Devon are isolated and which they will all need to enter, eventually. Finny isn't just ill-equipped for the war, he's ill-equipped for reality.
In a way, then, Phineas needed to die for the story to reach its logical conclusion. Men like Finny don't exist in the world; they can't, because they're simply too good for it. Few relationships at Devon aren't based on rivalry, Gene tells us, which is why he's so disturbed when Finny removes himself from competition. Finny, with his fantasies and naiveté, is on a higher, separate plane from the rest of us. Either he will be corrupted by the world, or destroyed by it, and in this novel, it's the latter.
So, back to that ending. Gene's explanation of Finny as an exception to the rest of us is expected; but that last line of the novel isn't. Gene turns the tables, switches his focus from the exception to the norm, which he questions: "...if he was indeed the enemy." Maybe, he ventures, Phineas's outlook was the better one. Maybe enemies are fictional, enmity a mere self-infliction. Either way, the adult Gene is still questioning and trying to learn, which is an optimistic response to his Chapter One hope that he would someday achieve growth and harmony.