I honestly believe that he's the right person for the job anyway. What he did to the Jet Alone, for example... It was such an easy thing for him to do. He eliminated the competition in a blink, all while making the EVA look better in comparison. He also knows how to deal with Seele and get funds. Heck, we was directly antagonizing Seele and making them pay for his stuff at the same time. Not only that, but he's great at improvising. The way he disposed of the Spear of Longinus was really smart. It was obvious that he was just messing around with Seele. Still, he had a great alibi... Last but not least, he knows how to select the right people to work with him and also, of course, manipulate them. No one person is good at everything. A good leader knows how to bring the best professionals closer.
He's the commander, not the cheif of operations. Gendo chose Misato because he knew she was better than anyone for that particular job. But, at the end of the day, he's still her boss.
Just sit here and waste your precious time. When you want to do something, don't do it right away. Don't do it when you can. Read my posts instead. It's the only way to live a life without regrets.