I don't think Parikia is "bad" in any sense, and frankly am puzzled by the title of your post. Parikia is the island's captital, and has the amenities of which all Parians depend, therefore making it a little more "city-like" than other settlements on Paros. It's the hub for the island's bus service, so getting around is easiest from Parikia. The Ekatontapiliani Church is probably the most beautiful in the Cyclades, and nearby the church is a small archaeological museum.
Naoussa, I'll have to say, is more picturesque, with several nice beaches in Naoussa Bay, all accessible by taxi boat from the harbour. It's also a little closer to the string of sandy beaches on the eastern coast. If some people prefer Naoussa, that doesn't make Parikia "bad". It's not an "either-or" situation, as there are many other nice places to stay on Paros.
That said, I prefer staying on Antiparos and taking an occasional day trip to Paros. I can be in Parikia in 30 minutes, and from there take the bus to Naoussa, Lefkes, Piso Livadi, Drios, Aliki, or just about anywhere else on Paros.