I find it hard to come up with a lot to say about Rooter both because he gets so little screen time and because so much about him is clouded in mystery. Regardless, I'll at least try and come up with responses for the two prompts:
1.) Personal thoughts on him and his scene aside (I'll get into that below), I think that it was for the best that the scene was added given that it does provide a bit of welcome recuperation after two back-to-back scenes of savagery/mass destruction and emotional devastation respectively; at the same time, I'll admit that I don't think it flows extremely well with what comes after, given that it is immediately followed by another scene of levity with the baby pterosaurs where Littlefoot isn't any better off emotionally than he was before his talk with Rooter. In that regard, I think it could have been cut out of the movie without much consequence.
That said, I think that the movie is better off
with the scene given how powerful it is; dare I say, I find it even stronger on an emotional front than the scene that precedes it.
2.) For as little time as he gets, I do get a character out of Rooter; though he's typically gruff and belligerent and has more likely than not been through some serious stuff throughout his long life, he knows when to let his guard down and impart wisdom and sympathy. Despite his rough edges, he is very likeable; I'm inclined to say that he's one of my favorite characters in the franchise, and I think that, if he was handled well, he would have been a very welcome addition to a sequel or two.
On that note, I think
VI would have better if it dropped the Lone Dinosaur and Saurus Rock guff and the focus on the Great Valley and instead focused on Rooter and his backstory with a slight western vibe.
I am wondering is Rooter the narrator or is it a coincidence that their both voiced by the same guy? 
I they just had Rooter be voiced by Pat Hingle because they already had him on board when Rooter was implemented, but I do like the prospect of Rooter doubling as the narrator, even if that idea isn't entirely solid given that he and the narrator's inflections are a little different.