There are a couple of reasons. The main was is that Greg Weisman was no longer working on the series. While Greg himself would tell you that it took tons of extremely talented people working together for Gargoyles to happen, he’s the one guy who has the most right to be called the creator of the show. What I’ve gathered from what Greg has said online is that Disney was looking to get Greg off of Gargoyles for the third season - which was called The Goliath Chronicles. Why this was happening I don’t know. And keep in mind that when I say “Disney” I mean "someone or some people at Disney’s TV division at the time, " since the company is not a single hive-mind. Anyway, Greg was going to have less creative control than he did on the first two seasons and his schedule for delivering episodes was literally impossible to meet. (Greg has said that the first script was due before he was even offered the job.) So despite his love for the series, Greg declined, though he did agree to write the first episode of the new season. And once the new team get in place, the schedule suddenly became much more reasonable and the new team got all the creative control that Greg had been denied.
Greg has said that he regrets leaving the show in hindsight, but I can certainly see why he did it at the time. And he did eventually get to do the Gargoyles comic, where he had far more creative control than he would have on The Goliath Chronicles.
Even though the schedule got more reasonable after Greg left, what I’ve read from people who actually worked on the show suggests that production was still rushed. I’ve heard people from the crew say that there wasn’t enough time to really look at the previous episodes and get a good sense of the look and feel of the show.
So what ended up on the air was a very mediocre third season. The first episode that Greg did - called “The Journey” - is pretty good, but you’ll probably notice that it looks different. Like most shows that were animated at multiple overseas studios, Gargoyles had its great looking episodes and episodes that didn’t look so great. The Goliath Chronicles - what I’ve seen of it at least - seldom gets past “okay” in the animation department. But what’s especially disappointing is how much of what made the series particularly special is gone. While you do get call backs to characters from previous episodes, the continuity between episodes is all but nonexistent. Everyone seems to forget everything that happened in all the previous episodes by the time a new one starts. Nothing changes until the very last episode. Plotlines from the first two seasons are dropped without explanation. Characters become less dimensional. If you watch "The Journey, " you can see storylines being set up for most of the main characters and while most of these are followed up on, that’s about where it stops. Rarely, if ever, is any characterization from the previous two seasons drawn on. Overall, the show stops being as epic and as smartly written as it once was and drops down to a level much closer to average.
There are some good ideas in TGC, some of which are drawn from ideas Greg had for what to do in a third season. And most - if not all- of the original voice actors stuck around, so there’s that. But since “The Journey” is retold in the Slave Labor Graphics comics, which Greg wrote himself, there’s no real need to watch any of the episodes. You’re welcome to do so if you want to; I believe they’re all still on YouTube. Just keep in mind that what you’re going to see won’t be up to the standard of the first two seasons.
I’m in love. Really, I’m ordering the action figures. I’m. In. LOVE. With a TV show. And I hate TV. 
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