I know that his passive would give him MR, Armour and AP, but then they changed it he will not gain any Mr by the souls..yet he still does not gain per lvl...why?

Because there are a ton of champions that don't gain MR per level.

55 in total.

Ahri, Anivia, Annie, Ashe, Brand, Caitlyn, Cass, Corki, Draven, Elise, Ezreal, Fiddlesticks, Galio, Gragas, Heimer, Janna, Jayce, Karma, Karthus, Kennen, Kog'maw, LeBlanc, Lulu, Lux, Malzahar, Maokai, Miss Fortune, Morgana, Nami, Orianna, Poppy, Ryze, Shen, Singed, Sivir, Sona, Soraka, Swain, Syndra, Teemo, Thresh, Tristana, Twisted Fate, Twitch, Urgot, Varus, Vayne, Viktor, Vladimir, Xerath, Ziggs, Zilean and Zyra.

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they felt a champion that got free ap and armor getting MR as well was a bit op i guess.

Ranged champions pretty much don't get innate magic resistance past 30 barring their abilities.

Except for Kayle. She's flexible like that.

I can see why Thresh might have scaling MR. He's a support/tank like Taric, who does get scaling MR.

The argument that Thresh is ranged is rather dubious, as really he's only 'ranged' during the laning phase, at which point scaling MR doesn't make a big difference. Late game all of his abilities function best when he's right in the thick of things, so he doesn't really get to take advantage of his ranged AA.

personally I think it make more thematic sense for Thresh to gain Mres instead of armor from souls. When I think of souls I think supernatural.