I always thought it would have been interesting to get a few more episodes out of the Jackie Sr. character. And while i get that his death is what sets the plot of season one in motion (Tony vs Uncle Jun.), i still think he would have been a strong character to contrast with Tony (as JCrusher points out).
While i do think the series is perfect the way it is, and i wouldn't/couldn't do a better job, i wonder if it would have been interesting to have season one's story like spread over the first two seasons. You get one season of Jackie's rule/cancer, ending with his death and Tony and Uncle Jun. being at odds. You follow that up with season two where Tony lets Uncle Jun take over to be the lightening rod. The same events from season one can still happen, just spread out a bit more!