This is...interesting. Metal Mario and the others 2 Caps do not protect Mario from falling damage. Metal and Invisible are just immune to attacking damage. If Mario had all three caps on at the same time(impossible in the games without cheating, mind you), then he'd be unbeatable. For a while, anyway.
Even Super Mario and Giant Mario just aren't as strong as Super Sonic. Bowser has gotten literal invincible status in the first two Paper Marios. The first one is his Star Rod power, and in the second one, you go through variations of the first courses in Super Mario Bros. as Bowser and he gets bigger with every mushroom, soon making him invincible. He literally glowed yellow.
Anyway, nobody truly went "Super" in the Mario series(by Sonic versions, anyway), though some have gone close.
Sonic mostly has a stamina advantage over Mario, while Mario has an item advantage, to an extent, anyway.
Physically, Mario is stronger, as he's more comparable to Knuckles(except for the jumping power), so Sonic is somewhat weaker in that aspect. Some could argue it in Sonic Battle terms, as Mario is the all around fighter having basic stats(Attack/Strenth Support 5, and no Other Support, as nothing makes sense)
Mario himself hasn't had an official fighter dedicated to his direct series, so comparing fighting skills isn't really possible. For the most part, they'd be considered equal as they are both the basic fighters.