I own eight Meeples of each of the following sets: Zombies, Princesses, Astronauts, Ninjas, Pirates (not the new ones), Monkeys, Monsters, Soldiers and Outlaws. I like the idea of collecting all of them but there's only so much you can do with them once you've got them and they're not cheap (especially if you live overseas).
The colour matching is tricky. Some are better than others so the Zombies go well with the green follower set and the Monsters go well with the blue follower set etc. The Princesses however are pink and the Monkeys are brown. I can get the pink and brown follower sets from Cundco to go with these but it seems like a lot of trouble to go to just for the sake of matching colours and the standard-sized Meeples from those sets wouldn't be used. I have no idea how I'd try to match some of the more recent additions to a set of coloured followers as they don't seem to have a single colour theme. You could try to be artistic about it but then you find yourself in the situation whereby you're trying to paint a Caveman builder/ pig/ mayor/ wagon/ barn and you start to wonder where your life went wrong...
The other problem is that because the character Meeples are all mega-Meeple size, you can't easily distinguish between them and the follower that represents the mega-Meeple. This can be solved now that there are the super-mega-Meeples but it's all extra expense.
In summary, I'd say that I really like the extra character Meeples and they do add a bit of fun. They're difficult to include in serious games though so think before you buy!