I'm looking to do a day trip from Paris (possibly stay over night but haven't narrowed it down yet). I can't decided on what city to visit. Bruges? Brussels? Ghent? Clearly Brussels is the "easiest" to get to but I haven't read anything that seems outstanding that would require a visit, but I also haven't done a ton of research either. Main interests are churches, cemeteries and botanical gardens. What's your favorite city in Belgium and why?
Belgium is pretty far for a day trip from Paris, nearly an hour and a half to Brussels by high-speed Thalys train. Bruges and Ghent would take longer. I don't have a favorite city in Belgium but good day trips from Paris might include Chartres, St-Denis (really just a suburb trip), Versailles, Fontainebleau, Reims, and Giverny. Others will have other ideas. Ina Caro's Paris to the Past describes lots of destinations reachable by train, most of them day trips.
For a day trip that involves a spectacular cathedral Chartres is hard to beat and a lot closer than Belgium.
Not sure if they count as day trips since you can get there on the Metro, but you might be interested in the Domaine de Saint Cloud or the park at Vincennes.
Lille is the furthest I'd consider for a day trip, but doesn't match your interests (the draw is museums and general city architecture). Brussels is doable at a stretch but it's far from the most interesting Belgian city. Chartres mentioned above is a much more solid recommendation!
Bruges for sure. Lovely canals, great cafes, chocolate, very walkable. Easy train ride. You are correct on your Brussels opinion.
2 days - half day in Ghent to start, then overnight and next day in Bruges
the best of Belgium