These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
How much you end up sympathising with him is, of course, up the the interpretation of the audience. Either he was a pawn in God's/Jesus' plan, a pawn in the Pharisees' plans, or misguided but ultimately chose his fate. (Or a mix)
Word of God from Tim Rice says that his aim as far as presenting Judas' character was more to with showing what he might have done in the same situation rather than making him interesting.
Pontius Pilate was also given some different perspective. In the musical he does not want to execute Jesus, thinking he is just another nut case who doesn't deserve death, and is utterly baffled why the mob wants him killed. He only goes through with the execution because he was given no other choice.
Though a similar impression is given in the Bible. That or not wanting to be bossed around. Many, many adaptations have been made over the centuries, in which Judas, Pilate, and/or the Jews have been blamed to a greater or lesser, sometimes very extreme degree.
In the 2000 film, even Jesus gets this; he comes off more than a little selfish in response to Judas in his early scenes, when Judas is protesting Mary's spending money on expensive foot ointments instead of the poor:
Jesus: There will be poor always, pathetically struggling; look at the good things you've got!
...You'll be lost, and you'll be so sorry, when I'm gone!
Awesome Music: The soundtrack topped the charts before the play came out.
First Installment Wins: Fans of the original LP concept album point out that it set the standard for all subsequent versions.
Literally, in the case of the vocal score, which in many places merely transcribes what was performed on the original album.
Hell Is That Noise: The overture starting out the original 1970 album begins with an acid guitar lick with a sinister Asiatic purr (perhaps representing traditional Middle Eastern music) that can be very unsettling - even spooky - to Western listeners. And that's even before the "horror movie" synthesizer kicks in...
A few of the live productions play up the gentility and respect in their relationship - they're like brothers.
The 2000 version seemed to do this as blatantly as possible (some would say it was turned Up to Eleven). All the apostles wore tight ripped shirts, leather pants, and very frequently caressed and hugged each other. While the women all wore pretty modest ankle length dresses and their hair held in a ratty bun.
To compare, in the 1973 version Judas' kiss of betrayal is Judas sneaking up from behind, giving Jesus a very quick light peck on the cheek. In the 2000 version, the two are looking each other directly in the eyes while crying. Then Judas gives him a deep, long, smooch and Jesus responds by briefly wrapping his arms around him before Judas pushes him off.
In the 2000 version of "Heaven on Their Minds", Judas pleads to Jesus while they are alone together, with lots of Judas getting into Jesus's personal space, and hesitant, delicate touches to Jesus's bare skin. Compare the 1973 version of "Heaven on Their Minds" which has Judas overlooking the group from a distance and talking to himself.
And then there's the bit where the last straw before his betrayal was catching Jesus and Mary Magdalene in a compromising position.
It's also arguable that the 2012 arena tour does this to a greater extent than the 1973 film... Probably not the 2000 one though. Some of the looks exchanged between Tim Minchin's Judas and Ben Forster's Jesus (or even just glances in the general direction of the other character) could easily be classed as 'longing'. Add to that Minchin's heartbreaking reprise of "I Don't Know How To Love Him" during "Judas' Death," and the fact that during "The Last Supper" some of the apostles genuinely look as though they're watching a couple have a screaming row..
Pilate: What is this new respect for Caesar? Until now it has been noticeably LACKING!
Narm: In the original album, during "Pilate and Christ" when a Roman soldier says "Someone Chrois', king of da Jeeewwwsss" in the Cockney accent.
The bizarre facial expressions made by Simon during "Simon Zealotes". The portrayal is less "violent, rebel agitator" and more "stoned, dancing hippie." Made even better by Judas' reaction shot, which can only be described as "What is this I don't even..."
You can even see Christ cracking up a little when Simon starts singing in his face. Corpsing?
It doesn't get better in the 2000 production, given Simon's frosted tips and the flamboyancy of some of his gestures.
The 90s Aussie production in spades. Strange Thing Mystifying sounds like a hair metal anthem.
The potential for Narm in "Heaven On Their Minds" is very strong, especially the first cry of "JEEEESUUUUS!"
Nightmare Fuel: The Crucifixion and preceding torture in the 1973 version.
The stage version includes a sequence so traumatizing that it's the visual/musical equivalent of swallowing an ice cube too fast. Immediately after performing the first half of "The Temple and Lepers," Jesus is accosted by a whole horde of lepers, cripples, and various other blighted folk. Pretty heart-rending in itself. But did I mention that they are covered in spider webs? That they're so wrapped in rags that you can't see their faces? And that they graphically describe all their injuries and infirmities in song? True, it's not Michael Jackson's Thriller, but it's pretty grotesque in itself. You can hardly blame Jesus when, in a What the Hell, Hero? moment, he screams: "HEAL YOURSELVES!!!"
Not forgetting that the song they're singing? It's the same tune as the merchants', only... different. And in 7/8 time, one of the most unsettling time signatures.
In the 1973 movie, the flogging itself is nasty enough, but then there's the intense music that goes with it, and Pilate's voice counting out the lashes. He sounds almost elated. Then when we see him trying to compose himself, he has an expression that could be aroused or disgusted or both.
Strawman Has a Point: Caiaphas and Annas are sitting on a powder keg (the people hate the Romans and are looking for any excuse to rebel) and see Jesus as the equivalent of a lit match in the powder keg. In Real Life, less than fifty years after the Crucifixion, the Jews did rebel...and got utterly crushed.
The Woobie: Mary Magdalene. Depending on the production, Jesus and/or Judas could be as well.