There's no strong reason to expect evolution to be optimal at anything. It's a process of gradient descent. If the particular thing you think it "should have" invented is behind too high a wall, oops, evolution never finds it.
And there's a high wall. Even if it's in P, calculating the structure of a protein from a functional goal is going to be energetically expensive on the scale of a cell. That's energy the organism could have used for eating or reproduction instead. And before that you have to biochemically represent goals for a protein, and match them with outside stimuli. More complexity, more energy. It doesn't seem worth it; life is already shockingly adaptable. Oh, and if you want arbitrary organelles, multiply all that by 10-1000.
And there's a high wall. Even if it's in P, calculating the structure of a protein from a functional goal is going to be energetically expensive on the scale of a cell. That's energy the organism could have used for eating or reproduction instead. And before that you have to biochemically represent goals for a protein, and match them with outside stimuli. More complexity, more energy. It doesn't seem worth it; life is already shockingly adaptable. Oh, and if you want arbitrary organelles, multiply all that by 10-1000.