In the end, this episode probably did too much too quickly. So much happens in this episode that it probably would have been served better by an arc similar to the one that started season 6. The Cardassian government falls, the Klingons declare war on the Cardassians, the Federation's alliance with the Klingons breaks down, and Worf is introduced, all in a two-parter. It works, but it shakes up the status quo so violently that the rest of the season is almost a let-down for sticking to the new status quo. It's a ginormous event episode in a season that otherwise lacks them. Spreading the wealth over a couple of episodes might have been a better way of going about things.
I don't think a six-part arc would have worked for it. For one, TPTB obviously weren't ready for something of that magnitude. Second, six parts might have been pushing it. I think a three part episode, which the show had already done, would have been more suitable.
Still, The Way of the Warrior
is easily one of show's best episodes.