Rouen versus Honfleur

Cannot speak for Rouen but Honfleur is peaceful, bucolic, relaxed and a great place to see plein artists at their craft. The river cruises come in also. Delightful place to visit.

When is the trip? How much time to you have?

Honfleur gets a fair number of tourists during high season, but at the time of my visit (July 2017) it wasn't so overwhelmed as to be ruined by the crowds. Just expect it to be quite touristy. A few hours might well be enough for you in Honfleur.

Rouen is about 15 times the size of Honfleur (pop. 110,000 vs. 7,500). It was heavily damaged during the war but has a large "historic" area extremely well-reconstructed in the old style; in much of that area there aren't very many tourists. There are several interesting museums. You could fill a full day in Rouen.

The experiences are very different. If you're driving, we'll need someone else to comment on how that might affect your visit; I am a public-transportation person.

You are asking us to compare "apples to oranges." Both cities are different from one another. How long would you have for the city of your choice? There's more to see and do in Rouen.
I've been to both places. Honfleur is visually stunning, as JS mentioned. The harbor is so picturesque, inviting one to linger at an outdoor cafe and people-watch. It wouldn't take long to "walk the entire town." It is much smaller than Rouen.
Rouen is not as picturesque as Honfleur, but it has a lot of history. I appreciated our time there.
Joan of Arc was burned at the stake here, marked by Towering Cross.
Monet painted the Cathedral many times in various lighting. There's a light show at the cathedral during the summer months.

A lot depends on when you are going, where you will be coming from/going to when you visit, and what types of things you enjoy seeing. I loved both of them but they are so different in so many ways. Rouen is a big city but the old center is very nice and compact. History wise it has the connection to Joan of Arc (she was burned in the square here), the cathedral is wonderful and if you're a Monet fan it's where he stayed and painted his series of works on the cathedral in all seasons at all times of day. There are several museums to visit and really deserves a day or two and an overnight. Honfleur, on the other hand, is a much smaller seaside town best visited in the summer. It has been a popular vacation spot for centuries and was particularly popular with the Impressionists and other 'plein air' painters. It's small, touristy, artistic, scenic, and has numerous seafood cafes on the waterfront.

I have stayed overnight in Honfleur on two different trips, and spent an afternoon there on a third. I consider it one of my favorite places in France and would go back. There are a couple of nice museums, plus the harbor, an interesting church, and quaint streets to wander. I have only spent an afternoon on one trip in Rouen, but would definitely consider going back. Since I drive, my main consideration is accessibility, so I frequently avoid larger towns. It has been several years, but I don't remember either Honfleur or Rouen being overly crowded with tourists - we were there in September.

I'll add my vote to just seeing Honfleur for part of a day. I visited in early May several years ago on a Road Scholar tour. As we got off the bus our guide noted there were 6 or 7 river cruise boats docked so warned us to allow sufficient time if we were going for a restaurant lunch as things would be busy and crowded. He was correct. It also happened to be pretty hot the day we visited (well I don't tolerate heat well so others may have felt comfortable) so I headed out to the beach to see if I could catch a breeze. The walk thru the park out to the beach was interesting and then walked on the beach long enough that I could add "hearing a cuckoo" to my Birding life list, lol. I did not get to the museum (closed for lunch during the day) but did see the double nave church and walked around the interesting old town on our walking tour of the area.

We also spent 2 nights in Rouen, so had a full day in the city center. I did not get everything seen but it also started bucketing rain in the afternoon which drove me back to the shelter of the hotel.

I'd vote for more time in Rouen.

Rouen is a big city. It has a massive old center with lots of medieval buildings. There's a connection to Joan of Arc (where she was executed). French cities always have a lot of activities and restaurants to keep you entertained.

Honfleur is a relatively small port town with quaint buildings, lodging and dining.

Maybe the question is how long do you want to visit? If you only want to spend a morning and get lunch before moving on, Rouen would be rushed and Honfleur would be relaxed. If you plan to stop for a couple days, Honfleur would be a complete break primarily enjoying views while Rouen would have sites and activities.

As Brad said I’d think time is key. We spent three nights in Rouen and a day while driving in Honfleur and had no regrets. The Rouen Cathedral and the Sound and Light show alone would take me back.