Researchers at ETH Zurich are well on their way to solving those problems with their Sepios robot, though. As you'll see in the video below, the cuttlefish-inspired creation undulates its four fins in tandem to move in any direction, even through obstacles (such as seagrass and metal frames) that would trip up other animal-like automatons. It's quiet, too, so it can float near real fish without immediately causing a panic.
Sepios got its first real field test last year, and the ETH crew is now focused on getting the machine's sensors (including the camera, distance-measuring laser and depth sensor) to talk to each other more effectively. So long as development continues hiccup-free, this uniquely shaped rover and its successors could be very helpful for filming and studying undersea life without disturbing the very conditions you're trying to observe.