My roster and Iso situation look like so and the question is which, if any, of my characters would you level. I’m hesitant to level C. Mags given his supposed impending nerf.
Your team isn’t strong enough to consistently win 3* covers (top 5), so I’d work on building up your 2* characters. C. Storm/Daken/MN Mags/Thor are all pretty good targets to level given your roster. I would wait til tomorrow to see what characters get buffed for the pve event so that you can plan accordingly. Daken probably won’t be an option for the heroes tournament tomorrow, so your best bet might be Thor and C. Storm.
Is it worth it to take Thor to 46? Would it be preferable to take 2* Wolvie to 61, as I can or is he just too weak in his current state?
He isn’t weak, but you already have a high level Daken, and 2* Wolvie is more of a sidegrade to Daken now as opposed to a direct upgrade like he was before. I didn’t realize that your Thor had so few covers: he probably isn’t worth getting to 46 only. In that case, I’d just wait until tomorrow and see then. If Thor or Wolvie are buffed for the event, then that might be enough of a push for you to invest in them: they’re definitely going to be featured in the hero tournament too, so theres that to consider.
c storm seems a safe bet, with the many recent events that have her buffed almost constantly.
Finish C.Storm, finish Daken. Level up buffed characters in today’s hulk event to level 50, then more if you want.
I would prioritize Thor over 2wolverine. Reason being that Thor is more useful from a utility perspective (generate AP colors), still has damage potential, and is more effective than 2 Wolv on defense.
If you get blue C. Storm covers, I’d recommend changing to 5/5/3. Her blue is absurdly good when buffed or when combo’d with MN Mags
Holy Heck man! Where did you get all that iso?! 
From last night to now I’ve gone from 145k to 160k
Farming LRs is a good way to get 1-2k iso for 5-10 minutes of work every 2 hours. I’m up 20k iso since the LRs started.
What this guy said. I just happen to be a hoarder.