Having played many formats, I disagree completely because even with one division, you still have the quirks of the schedule (who you play WHEN, not just who you play).
Having divisions gives realism and, especially in dynasties, gives a lot of benefits. You have the natural rivalries that develop. Like in real life, when you are in a division, your team IS affected, and may make roster decisions, based on who is in your division.
The difference, from my experience ahs come down to scheduling if you REALLY care about making it right.
What we have done in a few leagues I am in is:
1)Doubleheaders-You can argue triple headers all the way to all play, but a very good balance, IMO, to realism and fairness is to maintain H2H and doubleheaders DO smooth things out so that its not always about the bad luck of playing the hot team or career day guy, or the good luck of catching the guy that was on a heavy bye week. Over the course of 13 double headers, its pretty normalized.
2)No generic scheduling-I never can understand why people are willing to do the super generic schedule of "play all your division, then play everyone else, then play all your division again". Those kind of schedules just suck and they can really affect things more than anything else. If you are a team that plays in those leagues, a hot start lets you coast in your division, while a bad start has you out of it by October. Yes, it will take some time to develop a schedule the first time you do it for your particular league but once you have a template, it is very nice.
In my leagues that I actually have the input to do so, we have an original schedule that is very fun and realistic. We play doubleheaders and some teams DO open up in the division, while some teams don't. Some teams finish against divisional opponents, while others don't. Its very realistic. Some teams had one division game left to play in the last month while others are like the Cowboys and the Giants in the NFL and play each other twice during the last five weeks or so.
We also rotate the schedule to play strength of schedule so that the first place teams out of division may play one another twice the next year (making it more difficult to repeat in the division because the 3rd and 4th place teams get the luxury of playing weaker "out of divison" opponents while the top teams are playing teams that were better last year...just like the NFL basically).
3)Playoff qualifiers-The final thing we have done, just started this year, is to award the final #6 playoff spot to the team that scored the most points during the year instead of it being record based. This is our first year of doing it and going into the final week we literally have about 5-6 teams with legitimate shots of making the last spot and, again, its only one year of experience, but it seems to be a great equalizer because the teams that you would think are deserving of the last spot are the teams that are in the hunt for the spot. They all have the better records; separated by a game or two, and you can see cases for each of them when they played the career day team or played in a really good division, etc. Overall, it seems that they truly are the more deserving teams to fill that spot and not a team that benefited from pure luck.
The other side benefit we didn't plan for but experienced with this is that it kept so many teams in the running right to the end and that resulted in us not seeing teams have fire sales or just give all their players away and shift the balance heavily because they started out poorly (this is a dynasty league).
Overall, I think its those things and simply not just putting everyone in a big pool that makes for a better experience. I play in one league where in Week 4 an 0-4 team decided he was "done" for the year and gave up and he traded all his premier players for a bevvy of draft picks next year. Of course its fair and its just a strategical difference but the effect was the same: the team getting the players has not lost and probably won't and while all the other owners are good owners and will play till the end, this has been a lost season for most owners due to the decision of one. Since this is a contract/dynasty league, it affects a lot more than just this season. Perhaps with some different rules to keep the team in it longer, he would not have traded players.
