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.
Awesome Music: The soundtrack topped the charts before the play came out.
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. 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.
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.