I agree that the show has its flaws but I don't think these are the ones you brought up.

I actually like that new characters are introduced and I just accept that they were out of people's minds while they were in jail. the large ammount of characters added to the depth of the show I believe, and most of their stories and backgrounds fit with the ongoing action;

and more important, you shouldn't give "The Pilot" that much credit - I learned that it was made about 9-10 months before the rest of Season 1 and David Chase didn't even know if it would be picked up and he even wanted it to be made into a movie. it amazes me that HBO didn't free up the cash to reshoot it once it was picked up and I learned from message boards folks that when The Sopranos first aired they aired "The Pilot" and "46 Long" back-to-back, probably to make the viewer forget about the "flaws" (if you want) of the Pilot, mostly because it was dull and silly and it obviously didn't even fit with the plot of Season 1 - Tony is referred to as "the Don of New Jersey" several times and Sil doesn't even know who Artie Bucco is. plus, I always wonder that he is received as a surprise guest at the pork shop, which is named differently...

So you see, they fine tuned the plot once the show was picked up and in my opinion the first episodes do a good job overall as to introduce Tony and wrap up enough things about his job and personal life to make him likeable and interesting.