I have been to both, in fact took a group from college to the Flaine area staying in Les Carroz but we made it into Flaine most days.
Flaine in January should be pretty snowsure. Val Thorens is higher and has the glacier but I would be happy going to Flaine.
Both resorts are purpose built so think concrete blocks on the snow. Both are essentially traffic free.
The transfer time to Flaine is short assuming you are flying into Geneva 4 hrs + to Val Thorens. The best wat to get to Val Thorens used to be by train then a minibus transfer. Love that TGV .
Flaine is marginally better for beginners but both resorts have great nursery slopes and long confidence building easy blue runs.