I've been in a dynasty league for 3 years now. I like that we have 12 teams and deep rosters since it makes you really have to pay attention to the future more. For example: I've had Chester Taylor sitting on my bench for 2 years now, just hoping that he gets a starting gig somewhere.
Dynasty leagues can get as complicated as you want them (salary caps, contracts, transaction fees, etc...). I prefer the simpler versions that just keep the rosters from year to year but many people will say that salary caps are the way to go. You just need to hash out all of the possibilities with your league members and try what works best for all of you.
The best thing you can do is keep your rules fluid. Let the league adjust as you guys learn what you like and don't like. That doesn't mean changing rules in mid-season, of course.