It really depends what you plan to do for the 3 days.
Fallowfield is the student area/village and has good bus and rail links into the city, but there's not a great deal there if your not a student.
Trafford quayside is quite nice as you have a few shops, cinema, theatre and media city. It's walking distance to old Trafford stadium and there are a few hotels of various prices and qualities. You can get a tram from there into the city and it won't cost a bomb if u want a taxi back.
Trafford Centre shopping mall has at least 4 hotels, good transport links and is right next to the M60. There is loads to do there and free parking but it's a fair way from the city centre.
If you opt to stay in the city there are plenty of hotels to choose from and I would book sooner rather than later to get the cheapest prices. Always check the car parking pricesas they can be as much as the hotel.
Gmex premier inn is the best of that brand in the city but there are loads of hotels to choose from and it purely depends on your price range once you've decided where to stay.
Make sure you go to cloudwater at Piccadilly Gardens!