Stokes vs Flintoff is an interesting one.
Stokes is already 10 x the batsman Flintoff ever was, even at the latter's best. But he's unlikely to ever match what peak Flintoff did with the ball. Depends which discipline you think is going to be more important in this team.
Also worth considering that Flintoff's numbers only really stack up in a fairly narrow time frame (big hundred vs SA in 2003 up until the India tour of early 2006). Genuinely world class in that period, something like 41 with the bat and 25 with the ball. Either side of that (and there are a lot of games in there) - it gets very very ugly indeed.
I think Stokes wins you games on his own at times and he's the best team man you could ever want. Absolutely unreal attitude.