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yeah it would make sense. it's a common flaw in games though that you max out after everything is said & done.
sometimes being able to unlock all the skills earlier on and then unlock harder challenges as you progress would be better as it gives you a chance to learn the mechanics of the stuff you unlocked and improve with it as the going gets tougher.
the difficulty level is pretty flat across the game once all factions are on the ground.
Now up to the final mission on Spiderman (it tells you to finish upgrading before the final fight when you try to start it).
Have unlocked all abilities,gadgets and 80% of the gadget add-ons, all side-missions done except getting highest score on the challenge missions and the randomly activated faction crimes around the map. would say another 3-5 hours and I'll have 100% everything.
Still really enjoying it, the story progresses nicely, the boss fights are a bit on rails but fun, the challenge side missions are pure rage fuel and easily the hardest part of the game.
my biggest criticism is that by the time i've unlocked everything there will literally be nothing left on the map other than to fight randomly spawning groups of enemies which don't give any reward or to replay missions i've already done with no ramp up in difficulty.
overall though worth a purchase and will definitely pick up the dlc which i've seen for sale but not sure when it comes out or if it is out already.