The main argument that people have who are arguing for a linkage between jump shooting and FT skills is that a big disparity between these two is unrealistic (though conveniently ignoring the expert testimony of actual players like Larry Bird and Isaiah Thomas). Well, let's look at some stats, and ask whether there is a good correlation between shooting percentage and free throw percentage.
So I got the data for 452 players from the 2010-2011 NBA season from ESPN.com. Plotting FT% versus either FG% or 3 point% gives an unimpressive cloud, no sense by eye that there is a relationship between the two. And their linear correlation coefficients bear that out: r-squared for FT% vs FG% is a paltry 0.038. This might reflect the effect of big men, who can have high FG%, but have FT difficulties in. For 3pt shooting percentage is was better, but r-squared was still a small 0.132.
Because there were a good number of players who took very few 3 point shots, where they might have been screwing with the resulting correlation, I removed those players who attempted fewer than 0.3 three pointers per game. That made the r^2 =0.108.
Also, it's worth noting that the slope of these linear regression lines (despite the fact they didn't suggest a strong correlation) weren't very steep, between 0.38 to 0.52. This suggests that if you did link the two skills, it wouldn't be linked very tightly (a slope of 1 would mean that for a given % increase in FG/3P%, you'd get the same increase in FT%, 0.5 you'd get half that, etc.).
Now, one thing that was apparent from the data was that there were only 12 players who never made a FT (likely these guys took very few attempts), and then the next level of players, with the lowest FT%, started around 30% (there was nobody in between). This would support the suggestion that the lowest levels of FT be bumped up a little, if you believe that BuzzerBeater's main objective should be a realistic simulation of basketball stats.
I don't believe that, and never have in issues of game design where "playability/decision making" and "realism" are at odds. If you link shooting (either by jumpshot, or jump range, whatever, despite the evidence to the contrary) to FT, then you remove one of the strategic calculations that a manager has to make. "Should I train JS, or FT this week?" When that happens, things get boring IMO. Of course this was part of Charles's point.