Spear of the magus cost as much as executioner.

It's true, but Executioner doesn't give you 20 + 20% pen with two stacks. Otherwise every Physical god would be using it like every Mage already does. Even supports would get it if the passive didn't already work with allies.

all other class magical defense scale with levels.

You're right, I was mistaken and found this out about an hour ago. Magical Protection scales by 18 over 20 levels, and Phys Prot scales 58 over 20 levels. It's a huge difference, so the concept still applies.

Doom Orb is very cheap, in addition to actives being free now, so getting Spear can easily happen within the first 10-15 minutes, meaning Mages will be dealing true damage with all of their abilities for the entire game starting at that point. There is no reason to pick up Obsidian at all now, just as there is no reason to ever not pick up Spear as a third item. They should increase the passive stacks to 4 so the big advantage of taking burst mages over dot mages isn't there. Dot mages can have their setup interrupted and can be countered by actives like Shell, Beads, Sprint, Aegis. Mages like Zeus or Isis can break actives just using their normal kit with Spear in it. Broken.

You counter that pen and the power from that 3 items is not more than what a phys god receive in building the same amount of pen.

Just referring to what I said earlier in my reply here... There is a difference of 40 protections between Magic and Phys from levels 1-20. Meaning Mages naturally have a 40 pen advantage over Physical gods end game. To give them Spear 10 mins into game and this natural advantage is just too big of a swing and why you see burst Mages who can be strong all game chosen over ADCs. In fact, I wouldn't be surprised if we saw Mages just take the place of ADCs, and if they are ever picked, they would probably go in solo since they can be harder to gank earlier on.