That story had very noticeably cheaper looking CG work, indeed there have been many complaints over the years of the cheap looking CG used for rendering the Nazi occupied White House, or the Gorn in the MU episode.
And the season consisting of multi-part episodes wasn't because of budget, that was just how the stories were planned. Indeed, one of the writers, it was either Manny Coto or Mike Sussman even said the Klingon forehead storyline was originally only going to be a single part episode, the story just ended up getting so complex they needed to do it in two parts.
Indeed, many producers have said it's actually a myth that multi-part episodes save more money than doing standalone. It was cited as the reason why Doctor Who producer Russell T Davies chose to do the 2005 revival of the show as episodic rather than as serials like Classic Who was.