Anyway, this is why we have the current league and conference structure. Over time, these things do tend to balance out (as they have in the NBA historically as well).
The difference with the NBA are promotion and relegation.
My league is one of those in which one conference is much stronger than the other one. To give an idea, the mixed games ended 51-13 for my conference and the team ranked 5th in my conference has a better record than the 1st in the other conference.
Last season there was 1 promotion and 1 relegation from my conference and 3 teams were relegated from the other conference.
Considering that the teams relegated from an upper league are, on average, better than the average team and that teams promoted from a lower league are, still on average, less competitive than the average team... you see that the gap between the two conferences is more likely to increase than decrease.
My suggestion is, when possible, to always assign 2 new promoted teams to each conference and assign the team relegated from the upper team accordingly.