Judging by interviews, voice actors of characters like the Ghost crew members are given a run down of what will happen to them. Voice actors of characters that don't appear long enough in Rebels (like the Inquisitors) do not get this luxury (these characters also don't seem to have set fates like how the Ghost crew members are already planned to live or die at the beginning of the show).
Upon the topic of how long the show will run, Freddie constantly says that the show will likely last for more than 3 seasons, even saying in one interview that they could last 5-7 seasons. First Order even has him pointing out that it wouldn't make sense for Disney to cancel a show from a Cash-Cow Franchise. As long as there's are stories to tell, the show will continue, and once those stories are done, the show will end.
Freddie has revealed on his Twitch that by this, he means that Disney has given Filoni and co. a blank slate; the entire show was greenlit, meaning that it can be however long it needs to be, and that announcements about a season being greenlit are only to tell the press.
As of September 2016, they've been recording for Season 4 ever since July.
Back in Season 1, Freddie said that the story of Ezra getting his lightsaber would've been a two-parter, but this ends up being false. Either he was misinformed or this was the original plan for "Path of the Jedi".
Freddie Prinze Jr. mentions on Collider Jedi Council that in the finale, "Twilight ofthe Apprentice", once Kanan does a certain thing, he will have passed a Jedi trial, having already passed maybe two in Season 1. He's talking about how Kanan will lose his eyesight. In Legends, the trial is the Trial of Flesh, the third trial after Skill and Courage, before Spirit and Insight.
Sam Witwer has said that Maul was not entirely faking his weakness in "Twilight of the Apprentice", and while he doesn't show it his age is starting to catch up to him, hence why he wants an apprentice to pass on his legacy. He's also of the opinion (though he's not sure if the writers share it) that Maul sees Ezra as a sort of replacement for Savage.
In Season 1, Freddie's favorite character (besides Kanan and Ezra of course) was apparently Kallus. By Season 2 and Season 3, this list has extended to include Rau.
After Season 1, someone messaged Liam O'Brien on Twitter about returning to his role as Lyste, commenting that he should get a promotion. Liam replied that it'd be nice for Lyste, but probably not a good idea considering what happened to Aresko and Grint. This foreshadowed that Lyste would return in Season 2 with a promotion, as well as being a Butt-Monkey. Also became Hilarious in Hindsight/Harsher in Hindsight when Season 3 came around (which had not been recorded yet at the time), because while Lyste also returns, his final appearance is being arrested under a false charge of treason thanks to Kallus taking advantage of his ambition in that episode.
Right before Celebration 2017, Alan Tudyk expressed interest in voicing K-2SO in Rebels. Given that Season 4 was revealed to the final season and is now wrapping up production, however, it alas is not to be unless he joins the cast in the final episodes.
Alistair Petrie also expressed interest in voicing General Draven in Rebels as well, but unlike Tudyk, he stated this right after Rogue One premiered (and thus earlier on in the Season 4 production), so he's more likely to return.
In the promotional build-up for the show, Vanessa Marshall stated that Hera was personally hurt by Order 66. This was never explained, though it's easily inferable that hearing about Jedi, who were pivotal in helping her homeworld, getting executed and accused of crimes by the waning Republic would really shake her faith.
Filoni considered re-canonizing Starkiller from The Force Unleashed by introducing him into the show as an Inquisitor, but ultimately decided against it.
According to Freddie, the reason why some of the incidentals' lines sound Narmy despite them being capable of voicing the lines better is because the voice actors only did the lines as a joke and didn't think Filoni would actually put those lines in the final version.
An interview with Vanessa Marshall revealed that Jacen was conceived in the episode "Kindred", between Kanan and Hera's opening scene at dusk and their later scenes at dawn. Kanan's line "about what happened", which she cuts off with a kiss, was a reference to it which obviously couldn't be said onscreen.
even has him pointing out that it wouldn't make sense for Disney to cancel a show from a Cash-Cow Franchise. As long as there's are stories to tell, the show will continue, and once those stories are done, the show will end.