You can get good beer in any of these cities so that doesn't help you distinguish between them. I don't think Ghent is more attractive than Brugge, it is just different: a lot bigger, for a start, and it has a castle, which Brugge doesn't have. I suggest you google Brugge sights and Ghent sights - adding architecture if you want to - or check under "things to do" (left-hand side of the page) in each of the relevant TA forums, to determine which appeals to you most. For a first-time visitor I would recommend Brugge rather than Ghent, but in any case, the most convenient stops on a trip between Amsterdam and Paris would be Antwerp and Brussels, and these would also be the most interesting cities if, for example, you like art nouveau architecture (Zurenborg district in Antwerp, all over the city in Brussels). I do think you should see the Grand' Place in Brussels, but this does not require an overnight stay. And Brussels hotels are likely to be more expensive than Antwerp's.
I would therefore stick to your plan of staying 2 nights in Antwerp. Assuming that you get settled into a hotel/hostel by lunchtime on the Sunday, I would do a quick trip to Brugge on the same day. Being a Sunday you can get a weekend return for €15 instead of the weekday price of €28.20 (as a student, you could also get a "Go Pass 1" ticket for €13, that is €6.50 for Antwerp-Brugge and the same for Brugge-Antwerp; but only if you buy it online, see http://www.b-rail.be/nat/E/tarifs/tickets/gopass1/index.php - it's not available from stations).
On Monday, look around Antwerp: the diamond museum, for instance, is open, as is the zoo, and closing days are not a problem for architecture. You might like to explore Antwerpen Centraal station, and/or visit the art nouveau district near Berchem station: http://www.aviewoncities.com/antwerp/zurenborg.htm and/or wander around the little lanes near the cathedral, where you can see Antwerp's only surviving 16th C wooden house, in Stoelstraat, see http://www.belgiumview.com/belgiumview/tl3/view0001400.php4. The MAS Museum is unfortunately closed on Mondays but you might consider it worth seeing from the outside: http://www.mas.be/MAS-EN/Publicatiekanalen/Stad/Musea/Musea-MAS/MAS-EN/Startpagina-MAS-EN/Startpagina-MAS-EN-Hoofdnavigatie/Building-and-surrounding-area.html
Continue to Brussels on Tuesday morning. Get off at Gare centrale and leave bags in lockers there, then visit the Grand' Place which is about 5 mins walk away, and also the Galeries St. Hubert, close to the GP. Your Thalys ticket to Paris permits you to take a local train from Gare centrale to Gare du Midi for free, so do this (after picking up your bags) in time to connect to your Thalys departure - which will leave from platform 3, 4, 5 or 6 at Gare du Midi, at the Eurostar terminal end of the station.
You don't have time to get off the beaten track, or even to see all the main sights. You will have to be selective, and that means doing your own research so you can decide what you really want to see - which will also tell you how you want to divide your time.