Bruges and brussels

I think it is enough time for one city. I personally would choose Bruges.

I agree. Stay in Bruges the whole time, with maybe one day trip while you are there. What did you particularly want to see in Brussels? You might be able to see all you want to see in a few hours on your departure day.

It will help slightly if you say whether you are long-term resident in London, or if this is part of a trip from the US? I ask because my answer to your question is that you cannot omit Gent or Antwerp. But if you live in London, you can easily come for another weekend. Remember that Eurostar is much cheaper bought in advance and not at peak business-travel hours.

https://community.ricksteves.com/travel-forum/belgium/bruges-to-london-by-train

https://community.ricksteves.com/travel-forum/belgium/day-trips-from-brussels-besides-bruges-and-ghent

Don't forget that many (but not all) museums close on Monday. Brussels and Antwerp have so many museums (and so much to see on the street) that you can do either on a Monday. In particular, Bozar in Brussels and The Mystic Lamb (main attraction) in Gent are open on Mondays, AFAIR. If you like museums, it is not possible to see all of the best in Brussels or Antwerp in a single day. I consider it possible to see everything in Bruges in one day without slighting the place. But see below:

Of course, you have to check for Pandemic-Era hours anyplace you plan to visit. With only three overnights, it is possible you could stay in a single hotel and train to a second city. But that depends on whether you consider it essential to go to sleep and wake up in Bruges, for romantic reasons or to have some hours without daytripper crowds. Personally, that's not important to me, but it's important to many people who post here.

Why not stay in Brussels the whole time and take a day-trip to Bruges. Here’s what I would do:
Day 1 – check into hotel / Airbnb in Brussels. Visit Grand Place. For dinner order mussels, fries and beer at a place that does it right. Does not have to be at Grand Place.
Day 2 – Royal Museums of Fine Arts of Belgium. Sample chocolate at various stops.
Day 3 – day trip to Bruges, 1h by direct train.
Day 4 – laundry if needed and al fresco dining for lunch if warm enough. Do what you want to do.

Other than the Grand Place, Brussels holds no interest to me. Once seeing it, I’d move on to a more interesting city. Both Bruges and Gent have enough to see to fill 1.5-2 days each. I’d use one as a base and visit the other as a day trip. Either that just spend all your time in Bruges.

We are currently looking at Sunday to Wednesday, arrive midday to
Brussels from London on eurostar on the Sunday and depart at around
5pm back to London via eurostar on Wednesday.

That's really only 3 nights/2.5 (maybe) sightseeing days so I'd spend the entire thing in Bruges. Go directly there after arriving in Brussels, and return to Brussels after check-out on Sunday. If nervous about making it back to Brussels for your Wed. flight, then you could do Sunday-Monday nights in Bruges, leave later on Tuesday, and spend the pre-flight night in Brussels. You did't mention what time of year you're thinking of taking this trip?

You also haven't given us any idea what you are interested in doing/seeing while in Belgium but there's plenty to keep you occupied in Bruges IF you are interested in what she has to offer. We spent 4 nights/3.5 days there (minus a day trip to Ghent) and didn't cover it all.

We did spend 1 night in Brussels, and it didn't appeal to us as much as either Bruges or Ghent.

Editing to add: good reminder above about museum closures on Monday throughout Belgium; another good reason to spend both full days in Bruges. Some of the attractions which ARE open Mondays (or were recently) are Beguinage Ten Wijngaarde, virtually ALL of the historic churches (those alone could keep you busy all day), City Hall, the Belfry, the canal boat tours, and, of course, walks around the squares and many architectural points of interest. Do the museums on Tuesday.

I'd suggest staying in Ghent the entire time. Lots of people adore Bruges, but to me Ghent feels more real, and Bruges is more like a museum or a setting for a stage play. It's very pretty, and worthy of a day trip from Ghent for sure. Ghent is also more convenient - it's about halfway between Brussels and Bruges.

Wherever you stay, with only three nights, stay in one place.