Judging by what ARM had said of Sathyan's character, i guess he has got what he wanted. I guess it was largely intentional and except for the 'betermax' and couple of moments where he would be probing Vijay about the terrorist, Sathyan's character was never meant to be funny IMO.
Honest, one honest comment i have is, watching a movie like Thuppakki in theatres to watching at home first time, i guess makes a lot of difference.
But as you said, the movie is not without its flaws.