I think that Dion Restaurant has one of the best locations in town. Located near the city square with a view over Vardar river and the Archeological Museum, brunching at Dion is a must. At night, the lights of the new bridges provide a romantic tone to your dinner.
Their menu is abundant with Macedonian cuisine, but they do have some European options like pizza or pasta available. Local tip, Dion has a special price for pizzas on Mondays, Tuesdays and Sundays, so you might wanna try their Dion pizza or any other type. On Thursday, Friday and Saturday they have live Macedonian music. Also, for families with children, during the days with good weather, they have a playground near the terrace, which will make the brunching like a date at the spa. It can’t get better than that.
Since it is located in the center city, the restaurant is quite busy, so the service is slower, but my opinion is that it is totally worth it.