Well, you're clearly not watching the right anime, then. The best anime out there have almost no plot holes, at least not ones that people will immediately notice. You just gotta find them (there aren't many like that nowadays, so you may have to go back a few years).
My favorite anime right now is Steins;Gate - excellent plot with virtually no plot holes, even in spite of its complex time-travel theory
My favorite anime right now is Steins;Gate - excellent plot with virtually no plot holes, even in spite of its complex time-travel theory