Actually there was, when there were 3 divisions winners getting 1-3, there was always one weak division..
One of the ideas I had to help mitigate this factor was more of just copying another league (in this case the Arena Football League) than my own idea: for the purposes of matchups, don't give out the top three seeds to the division winners automatically (of course, the 1 seed would still always go to a division winner). Then, to give division winners at least somewhat of a reward for winning their division, guarantee them home ice advantage in their first-round series.
At the time I had that thought, I gave no consideration to the possible scenario where the worst division winner finished 8th in the conference, or any other combination of results would result in two division winners facing each other in the first round. I don't really have any ideas to solve that issue, except maybe perhaps bumping the division winner up one seed until you end up with first round matchups that don't involve two division winners against each other.
Another format that helps a bit was copying the NBA's format at the time (which they still might do). The team with the best record that does not win its division can get as high as the 2 seed if they have a better record than one of the division winners.
Obviously, none of these really apply anymore since we now have 2 divisions of 8 teams each rather than 3 divisions per conference. I suppose you could rearrange it to do 1-8 and assign seeds based on record alone, without guaranteeing the top 2 seeds to the two division winners, I guess.
Edit: by now, however, my opinion is that I don't really care either way. To me, the point of the playoffs is to crown a champion and nothing else. I'm not really bothered about the order in which the eventual champion has to defeat their opponents, nor how the matchups are determined along the way.