A few things to look at with your numbers:
1) you are comparing 25 games in a lockout season to full seasons. Lin has to play a full season with his "Linsanity" numbers to be able to compare to players who play a full season. Lin also has to produce Lowery/ Dragic numbers in a non-lockout season where he played sparingly while other players were playing 5 to 6 games a week. Lin definitely looked fresher, during the first couple of weeks of Linsanity, than his opponents (a perfect example was when he played against a laker team that played 6 games in 7 seven nights). Players bodies were breaking down after 5 weeks of playing this amount of games. Lin's body broke down after about 4 weeks of these games.
2) Since the Rockets play a style that emphasizes attacking the rim and 3's, Lowery and Dragic are above average 3 point shooters while Lin is below average, so they are more likely to have success in the rockets type of offense.
3) Look at the Assist to Turnover ratio. Kyle Lowery and Goran Dragic each average more than 2 Assists to Turnovers. Lin, even during Linsanity, has never averaged more than 1.7 Assists to Turnovers. This is the biggest criticism of Lin. His decision making. He is an average at best playmaker and his mistake come to light most late in games. Even though his TOs per game went down this year, his TO% increased to the point he had the second highest TO% among PGs who play 16 minutes or more. Like Steve Kerr and Peter Vescey both have said, Lin's optimal position on a team is a score first 6th man.
My point is that all three PGs had much better stats when they weren't playing for Houston. Houston already has Harden and Howard. Dragic, Lowry, or Lin at best would be the 3rd option. Agreed?
And Beverly matches up very well with Harden since he doesn't take many shots and Beverly's defense makes up for Harden's lack thereof, which means even less minutes at the PG position. Agreed?
So any PG playing in Houston is going to get less touches, less shots, and less minutes than playing as the 1st option in Toronto or Phoenix. Less touches, shots, and minutes equal less stats. Agreed?
By this reasoning, if we kept Dragic in Houston and Lin ended up in Phoenix instead, Dragic's numbers would be worse (with Harden, Howard, and Beverly in the fold) than his Phoenix numbers; and Lin's numbers would be better in Phoenix.
But probably the only way to really see if this is true is if/when the Rockets trade him to another team. I'm hoping that they keep him and figure out a way to integrate him in better, though.
If anything, I think the biggest positive change we could make would be to replace McHale with Stan Van Gundy. In my opinion, Stan is the best fit for our Rockets and probably the best coach out there without a team.