I dont think Spencer is such a bad matchup for Thor, neither Zero, Wolverine or Wesker.
Zero control the air-space but Thor has tools to deal with it, Mighty spark L for chip and pokes, Mighty Strike goes through the buster, one mighty hurricane and Zero is dead, etc. Zero zoning is not Thor main concern, it’s actually the pressure of his normals + teleports when combined with a fast beam assist with a lot of priority (Plasma beam for example), so if Zero can get the advantage it will be more about the assist than Thor losing to his neutral game.
Wolvie is very zoneable, his attacks are not jump cancellable and require him to be close, so blocked attacks can always be cancelled into XF for a Mighty hurricane TOD, specially the divekick.
Spencer has some holes in his offense, for example when he does the zipline square dash and call a beam assist, Thor can on reaction call his own beam assist and punish Spencer airdash with s.Mighty Strike H. Bionic arm is probably Spencer best tool here, and the annoying hitbox of the zipline, but beyond that its not so hard to play. My Thor bnb deal 1.000k with 1 DHC (as should the most of Thor bnb for the different team combinations), so if Spencer can kill Thor out of one touch (after of a LOT of work) the same can be said about Thor, mighty sparks L/M/H have a portion of unscalled damage, adding those beams to combos gives Thor the chance to strike some real damage.
Oh mr. Phiall and everytime Spencer do the zipline /command grab and catch Thor in the mid of a combo, do the Mighty Hurricane H motion in your pad/stick when Thor get back to his standing position, you will thank me later 
Again, as i said, it’s all about the assists game. For example Ammy gives Thor the chance to go into high-low mixups and fight like the top tier characters, so playing Thor with Coldstar makes him a real threat at close range, probably as dangerous as Viper or Firebrand. Strange bolts of balthakk enhance Thor zoning by A LOT, and punish some other assists, like hidden missiles, other beams, etc. It’s all about the assists.
As for Wesker, i’m starting to think he is overrated, all Thor has to do to counter Wesker is either maneuver around the gunshot zoning and counter with the Spark + zoning assist, or punish bad approachs with mixups / mighty strike + lockdown assist. Thor cannot XFC, Mighty Hurricane TOD Wesker on block though, Wesker can always use the 1 frame command grab -.-