Edit (April 17th, 2008) - To ansaris: Yes, I have read the entire series (I started following this series from volume 10; I suppose my experience with this series will be a little different, since I had access to the first 10 volumes from the start and thus was able to bypass the mediocre beginning circus arc in one go).
To be honest, I did not like parts of the ending (Hence the removal of this series from the top spot); I didn't like how all the characters had their own prospective final villain to fight (Yes this includes the circus crew). While this makes it more realistic in that the non-combatants had to participate regardless of skill, it just seemed too convenient.
I don't like how Shirogane yells "Les arts martiaux"/some move in French every time she fights - It just seems silly after a while.
This manga has a lot of characters (If you've seen the cast role at the end of volume 43). It wouldn't be prudent to go into everyone's background too much (Though enough is always given). Besides, the school scenes were more about Masaru's change/growth and his new interactions with his classmates and not about the individual classmates. They were mostly disposable characters solely for the purpose of showing off the new Masaru. And yes, I can believe his 180 change in character after reading the first 3 volumes.
Later on, the manga does provide explanation for why he's so talented at controlling puppets from the get-go, child genius reasons aside. It's a pretty big revelation so I won't ruin it here (Volume 27). His potential for a drastic change in character could be attributed to that as well, though that was never implicitly stated in the series.
Remember, the main character is Masaru (And Narumi for the first good part). All the other characters are side characters. But yeah, I didn't like reading about Masaru's arc until way later, when he finally leaves that damn circus troupe behind to figure out his past and why the inheritance was left to him (20+ volumes later, sigh). Narumi serves as a good buffer for the first 28 volumes of the series for people who don't like Masaru.
Eventually Masaru does shine through, mostly because he doesn't give you a reason to hate him.
Shirogane is like that because that's how she was brought up. If you read about her background later on (I think volume 24?), you'll understand. She's really not a deep character at all, but she does become a lot more lively by then.
The circus people's backgrounds does come into play at the end, but it's really not an integral part of the story.
Villains? Yes this series has a lot of automata. Most of them are fillers, I definitely agree with you there; but you don't really need background for automata when they're coming in droves. Besides, good villains do show up later, so that kind of makes up for it.
Granted, I'm rather partial to this series because I bought the series only by its cover (Well having read his others series Ushio and Tora helped a lot, but I wasn't a super big fan of that series).
Volumes 1 to 23 - Narumi takes center stage, Masaru takes back seat.
Volumes 23 onwards - Masaru and Narumi both share the stage equally.
Yeah the circus arc is kind of boring compared to Narumi's Karakuri arc. For the first part of the series, I was mostly reading it because of Narumi.
Berserk is my favorite series because of Gatsu, not because of the story.