I'm a beginner as far as FB is concerned. However, I've been reading for a couple of days about it, and would like to start a league with rules completely different from what you might know. I call it "FBlite".
Why? Although I like all kinds of games and riddles, I'm here as an NBA fan, and what I don't like about regular FB is that it has relatively little to do with basketball, and more with being able to exploit the rules of the game. In auction drafts, it seems that many people get their LeBrons for $90, add most of the squad for $1, and then play the FA market heavily. 87 trades later, they have a great team. For this and other reasons, I'd like to try something slightly different. I'll list the issues I can see, together with my ideas how to fix them.
Problem 1. There are 30x5=150 starters in the NBA, thus around 200 players that could become starters at any time. In most FB leagues I see there are 12 teams, thus 12x13=156 players. Meaning it's always easy to pick up a FA guy that might play 30 minutes tomorrow. I don't like it. My first instinct told me to forbid FA and trades, but then it's too boring some might say. So instead, how about limiting them, to e.g. 5 per season? Plus, what I really dream of is a very deep league: 20 teams of 15 players. Both those changes should also make it easier on those who don't have unlimited free time on a daily basis during the whole season. And since it's supposed not to take too much of your time, anybody could easily play his good old FB, and what I'm proposing here.
Problem 2. Most NBA rotations actively use about 10 players, i.e. 2 per position. That's how a basketball team is built. In order to give 10 guys their minutes, and still avoid injury trouble, I'd take 2x each position + 5 bench players = 15. Brings it closer to basketball, if you ask me.
Problem 3. Scoring system. I have no experience, so waiting for your advice. However, both H2H and roto sound a bit artificial to me, so I'd suggest normal points, with coefficients chosen in some kind of standard way. Hopefully a lot of them, to bring the game closer to basketball again. E.g. Yahoo lets me choose from 20+, and I'm sure there are some PhD theses out there giving you a nice set of those. (Right?)
Problem 4: type of draft. I started off by whining about how the auctions are far from realistic, so you can imagine that's the way I want to go. Snake is just boring anyway, right? And yes, I know this way the veterans will eat me for breakfast

Problem 5: when and where. I live in Europe, so I'm thinking Sunday 15h00 East Coast (12h00 West Coast, 21h00 CEST). Yahoo, ESPN, something else? Which is the best?
'nuff said. Give me some wise words of advice, and/or let me know if you'd like to try it.
Cheers!