If your long weekend includes a full Friday or Monday, you can get an adult and toddler ticket for Legoland for £12. If it doesn't include a ticket, you can get tickets on cereal boxes, hand wash etc for 2 for 1 tickets. If DC is under 3, they go free, so you'll only need to pay for one adult.
Sealife Centre is okay but only lasts maybe an hour at most. So I'd do Sealife first then next door to Legoland - my DS can spend HOURS there.
There's a Premier Inn at the Trafford Centre and plenty of restaurants inside the food court, and there's a soft play in there, too.
The Play Factor-e is incredible but more so for older children. A toddler would get lost in there and the price is extortionate!
If it's easier for your DP to be in the city centre for a hotel, a tram out to the Trafford Centre, or a taxi, is easy enough. And within the city centre there's the Museum of Science and Industry which is fab.
Also if staying in Manchester, you can get a train from Manchester Victoria station to Halifax station which is next door to Eureka! which is absolutely fantastic for kids. It takes 42 minutes on the train and it kept my son busy all day.