I think the difference in exterior ship design is ok. The Naboo royal ship is a yacht for the queen of a pretty wealthy planet, so of course it’s going to look flashy. And the Naboo fighters are probably not that great on a tech level, because they’re part of a planetary defense force. So they didn’t see much action. likely they mainly exist to be shown off, so they were made to look sleek and futuristic.
In the OT, you have a faction that’s basically keeping its old ships together with duct tape fighting a faction that employs very utilitarian and brutalist aesthetics for their ships. So there’s no room for sleek designs. I still think internal stuff like the Separatist ships having touch screens is dumb though.