The following is true for UBx STORM-combo-decks:
Those decks have 3 types of protection:
(1) permanent-hate (Chain of Vapor, Echoing Truth, Hurkyll's Recall, Abrupt Decay, Shattering Spree)
(2) discard (Cabal Therapy, Duress, Thoughtseize, Inquisition of Kozilek)
(3) chant-effects (Orim's Chant, Silence, Autumn's Veil)
The (1) category is meant to deal with our PERMANENTS (Thorn, Chalice, Thalia, Pyrostatic Pillar, sometimes Lackey).
The (2) category (discard) is the only kind of card that can deal with Mindbreak Trap, while it occasionally affects permaments that we couldn't play fast enough (like when they Duress you before Turn 2 or when you don't have the color-fixing for Thalia).
The (3) category - chant-effects - are most likely sided out in G2 and G3.
It is important to know what their maindeck looks like after G1, which is roughly:
32 mana-spells + lands
12 Cantrips
10 business spells (Infernal Tutor, Burning Wish, Ad Nauseam, Tendrils of Agony, Past in Flames)
6 protection spells
With only 6 protection spells (well, let's say it's 8 at max) they will likely only find 1 (if any) before they go off.
The same is true for you. You have 8 hate cards. If ALL of them are permanents (Thorns, Chalice, Thalia), then ALL of those cards can be dealt with by either bounce or ocassionally discard. However, if you split your hate up, you "force" them to have the right protection for your hate. i.e. Mindbreak Trap blanks bounce. Chalice blanks discard. Again: when your hate is solely permanents then they can easily bring in up to 6 bounce/shatter/whatever cards and they will ALWAYS have the correct card to deal with your permanent. If they draw a Chain of Vapor then it doesn't matter wether it bounces a Thalia, or a Chalice or a Thorn of Amethyst.
Plus, when you win game 2 with a Thorn of Amethyst, they might side out some more discard to bring in more bounce. Or vice-versa: if they lose G2 to a Mindbreak Trap, they might think about bringing Duress back in from the board to have more protection for your Traps. For storm-combo decks it's crucial to figure out what kind of hatecard your opponent has.
I know that Chalice is a flexible card in general and I would prefer Chalice over Thorn, ceteris paribus. But, Thorn does some magic vs. S&T decks, while Chalice is basically useless in this MU. That's why I suggested to run Thorn (in his case). Also, he said he didn't want Thalia. That does not change the fact that all cards are very good options for hating strom-combo. Another (of course less flexible) option would be 4 Mindbreak Traps + 4 Leyline of Sanctity (to protect your Traps from discard). However, that implies that you are lucky enough to draw both of them.
Keep in mind that I was only referring to storm-combo MU. I'm not looking at the respective card's value for other MUs.

