Episode 3 covered chapter 5 and most of chapter 6. In the original series, this was episode 6.
I'll make a list of the small opening details. The 1999 series and the manga had the Kiriko father navigate the trio to the Examination Hall in Zaban City. The 2011 series has the Kiriko son do so instead. The architecture in the 2011 series looks closer to the manga's version. I think that the 1999 series handled the restaurant joke better.
Though the character design of the restaurant chef is closer to the manga, the 2011 version removes his part-timer, and she's in the 1999 version. The 2011 version also gets rid of the free dinner the characters were supposed to get, which isn't in the 1999 version either.
For the underground tunnels themselves, I think that the 1999 series also got the atmosphere right. The dark ambiance, the glaring eyes. That's all missing from the 2011 show.
But the 1999 version fails at creating background characters. The people taking the Hunter Exam are given some pretty cool outfits, so you never know who might make it in the end in the manga. The 1999 series came out with some pretty generic characters, but we see some interesting contenders in the manga. The 2011 version follows suit and makes even the background characters look interesting.
Also, Beans shows up.
Tonpa. His introduction is just about the same in either version. So are his mannerisms. The way he introduces the contenders is different. 2011's version is closer to the manga, and the 1999 series doesn't have him interact with Killua and Hanzo.
Hanzo
Bourbon
Amori Brothers
Geretta
The juice scene is also added back in.
If you've noticed, Killua's personality is significantly different from his appearance in the 1999 series. In the 1999 show, he keeps to himself. He's quieter, shy, and typically always scowling. He won't tell anyone his name. It's different in the manga and 2011 series. Killua is much more sociable, which is in line with his personality.
I know that some of you were disappointed with Hisoka's entrance. Specifically, with whatever he did to that guy's arms. But do you remember how the 1999 series handled it? Somehow, Hisoka ended up sticking the man inside of a wall. It was a bloodless scene in the manga as well. His arms had just vanished. It's possible this scene could be edited for blu-ray. I can't say for sure though.
Personally, I like Hisoka's deeper voice. I always assumed he would have one when I read the series.
Satotz. For some reason, he can fly in the 1999 series? He sort of hovers down in the old version.
His character design looks kind of different. I like his alarm better in this one, though. His walk is also fixed to how it looks in the manga. The 1999 series had him sort of do it normally, but it always looked weird.
Since the entirety of chapter 6 wasn't covered, I'll save the main differences for next week. We should cover most of the stuff from chapters 6-8 and episodes 6-8.