The systems may be reliable, but they are still aging. The basic Soyuz design dates to the sixties. There have been upgrades along the way, but reliance on aging technology is never the best bet when so much new technology is out there.
Sure, new designs are nice. They're also expensive, and (unfortunately perhaps) no one's in a hurry to spend money on developing them. In the meantime the Soyuz works well enough. Besides, the newest technology is not always the best. From a US perspective, the main drawback of the Soyuz is not that it's old technology, but that it's Russian.