Of course, everyone hated the sequels to both franchises....To me, this isn't like making a sequel to Cinderella or Pinocchio. It could be more like a sequel to Star Wars or Indiana Jones of the Toon variety if done right. Just say no to motion capture. It doesn't work with classic toons.
As far as I'd go, I'd wanna see either a movie version of the second book, or something where Television hit, and old time toons are losing their jobs (something about 1959 would do). Think about it... they could have Rocky and Bullwinkle animated in there. Something where Roger has to take on a limited television animation job to keep carrots on the table, and it doesn't even do all that well. Something where Roger gets caught up in some criminal conspiracy, and his misery is the perfect motive to frame him for something, say the death of a TV animation producer.