CF is an easier and more common position for a young player to thrive in.
Midfield is far more sophisticated and requires more consistency and concentration. The margin for error is much smaller.
R9's decision-making was erratic at best and played in the weakest league of the three. Ultimately you can only beat what's in front of you and he had absolute freak statistics for a player of his age. Ridiculously well-timed runs in behind, pace to burn and the composure of a seasoned top level striker. Also hugely benefited from having Nilis alongside him putting chance after chance on a platter for him and help him become more mature when it came to decision making. R9 himself many times referred to Nilis as the best striking partner he has ever played with and learnt the most from. Nilis was to R9 at PSV what Bergkamp was to Henry at Arsenal.
I've never seen a player with Cesc's vision and passing range at age 16. Did all the stuff Xavi and Pirlo were praised for during their late '20s and early '30s. Undoubtedly one of the, if not the most natural play makers of the last couple of decades.
Whilst not quite as refined when it came to rounding off chances as R9 was at the same age, Messi was probably the most complete footballer of the three. Merking defenders in all areas of the field, creating, scoring - he could do it all and do it consistently at a very young age. Didn't quite have Cesc's passing range but was a lot more mature in terms of on-field behavior and general antics, which—in Cesc's case—continued to be rather cringe-worthy throughout his career.
At 16-17 all three covered different positions and played in different leagues under different circumstances.
Ultimately Messi, Fàbregas and R9 are all up there - there is no obvious choice.