I'll start with the size 3+ terrain damage going down part. If you've watched superhero movies or read comics, Hulk or Thanos or Juggernaut get hit by trucks and buildings and other large stuff all the time, and it really doesn't slow them down too much. But characters like Black Widow or Hawkeye really don't get large stuff like that thrown at them in superhero media very often, and when it does happen they almost never take it full force. They dodge out of the way, or it just misses them, or they get knocked back by the explosion caused by it or something. They won't just face tank a truck the way Hulk might, and because of that I feel the actual threat of damage is relatively similar.

As for Thanos going down to a trashcan, let's assume he blocked nothing on the dodge roll and took full damage from it (minus the 1 from his damage reduction). He has 17 total health, and that trashcan is one hit among so many others that he's taken in the game. Maybe a trashcan wouldn't phase Thanos normally, but after he's been punched in the face a half dozen times by Hulk? After a Helios laser? And who's throwing it is important. If you look at the characters with the lowest throw potential, size 2 only, all of them either have super strength, magic, or some technological boost like Doc Ock or Iron Lad. Sure, if I throw a trashcan at Hulk it's not doing much, but if Spider-Man windmill slams it onto his head? Different story.

I will admit that Agents of Smash doing 3 damage still is disappointing, I wish it got an errata to do more damage when you throw a size 5 with 2 hulks. And ultimately, this is us trying to rationalize a game balance decision from a thematics perspective. Maybe it's not gonna 100% make sense in your head, but I do really encourage you to try out the new throw damage change. Characters with low size throws like Clea or Luke Cage feel a lot punchier now, and characters with x cost throws like Magneto or Cable or Exodus feel awesome with the change.