All three Pokemon are good, and they work together well. Ivysaur isn't about killing really, though uair and dair are passable for that. Ivysaur camps extremely well, and it racks damage very efficiently while it does so and mega fast when it can sneak in Bullet Seed. I don't understand how anyone could say a character with that bair has safety issues; in general, Ivysaur can space well to make many of its normals quite safe to throw out, poke with, and generally rack damage.
Of course, Ivysaur doesn't need to kill really because Charizard does that very well and is next in line. It's really not that fair to directly point by point Charizard vs Bowser, but Charizard does have a lot of advantages (so does Bowser, but the point is there are a lot of good things about Charizard that aren't true about Bowser). Rock Smash does stupid damage and is seriously not that hard to land. Charizard's fair is flat out amazing air to air and can be used to keep him pretty safe. Charizard has a way better recovery than Bowser, and he can use his extra midair jump and gliding semi-effectively over the stage as well just for general mobility (also his glide attack kills absurdly low if you manage to land it, and it has no landing lag so it's pretty safe to go for if you're smart). Charizard has a stupidly fast dtilt that is easy to overlook but I'm pretty sure completely safe. Charizard has ridiculous grab range (as I recall, it's actually bigger than King Dedede's) and good throws that can kill. Charizard has that great usmash. Also, in general, Charizard has a lot of options that kill very, very well. All those kill move buffs on Charizard give him a ton of options to score low% kills and make him a nightmare for characters at high% which is exactly what his "I can't kill without stamina" and "my kill moves are way too slow" teammates need him for. Charizard also avoids the "big and slow" problem of taking damage way too fast at low% well. If he finds himself at low%, he's one move away from being a character who thrives in those conditions. He's not only pretty solid as an individual, but he has his holes filled by his team while simultaneously filling their holes. Charizard is one fantastic team player, probably a bigger team player than Squirtle and Ivysaur (who are hardly bad team players themselves).
And, of course, Squirtle is Squirtle, and remember he lost grab release problems as well as got a buffed Water Gun so he's actually better than ever. Remember that switching is faster so PT can flexibly shift between his teammates far more effectively than before (it is seriously hard to prevent PT from switching without exposing yourself to constant big risk).
I think you overrate Mario a bit still. Mario is definitely good, but it's not like Marth and G&W are the only two who can zone him. Meta Knight can do it too and quite well, and he has few tools to abuse other characters who have to worry about being zoned out. Like, Mario vs Sonic? This is theory fighter all the way on this one, but on paper it sure looks like this should lean toward Sonic. Mario won't be keeping Sonic out, and I find it hard to see his superior KO options outweighing Sonic's massive speed advantage and the fact that honestly Sonic is gimping Mario more than Mario is gimping Sonic. I definitely am not sold on Mario having overcome natural Ice Climbers problems. A character like him has few options to avoid being grabbed by the duo, especially as he has to overcome well placed walls of Blizzard to even attack their shield in the first place and ice blocks eat fireballs. Now, I'm not saying Mario has particularly bad matchups; he is a character who is probably pretty predictable to not have any truly awful ones. I just find it hard to say that he has only two slight negatives; I would expect to see him have several more. Slight negatives of course, he is definitely good, but I think more negatives than two.
As per the suggestion people are sleeping on R.O.B., that's plausible enough. Unless we screwed something up, his uthrow isn't really that good at killing (the idea is that it kills when R.O.B. can't land anything else but isn't what he wants to have to rely on), and I think you overrate just how much you get out of dthrow (though it is definitely a great throw). The things you're saying about his matchups being externally better anyway is easy to see; intuitively I'd agree with that. I haven't really seen anyone using R.O.B. much though; I'd definitely like to see more of him.
Of course, Ivysaur doesn't need to kill really because Charizard does that very well and is next in line. It's really not that fair to directly point by point Charizard vs Bowser, but Charizard does have a lot of advantages (so does Bowser, but the point is there are a lot of good things about Charizard that aren't true about Bowser). Rock Smash does stupid damage and is seriously not that hard to land. Charizard's fair is flat out amazing air to air and can be used to keep him pretty safe. Charizard has a way better recovery than Bowser, and he can use his extra midair jump and gliding semi-effectively over the stage as well just for general mobility (also his glide attack kills absurdly low if you manage to land it, and it has no landing lag so it's pretty safe to go for if you're smart). Charizard has a stupidly fast dtilt that is easy to overlook but I'm pretty sure completely safe. Charizard has ridiculous grab range (as I recall, it's actually bigger than King Dedede's) and good throws that can kill. Charizard has that great usmash. Also, in general, Charizard has a lot of options that kill very, very well. All those kill move buffs on Charizard give him a ton of options to score low% kills and make him a nightmare for characters at high% which is exactly what his "I can't kill without stamina" and "my kill moves are way too slow" teammates need him for. Charizard also avoids the "big and slow" problem of taking damage way too fast at low% well. If he finds himself at low%, he's one move away from being a character who thrives in those conditions. He's not only pretty solid as an individual, but he has his holes filled by his team while simultaneously filling their holes. Charizard is one fantastic team player, probably a bigger team player than Squirtle and Ivysaur (who are hardly bad team players themselves).
And, of course, Squirtle is Squirtle, and remember he lost grab release problems as well as got a buffed Water Gun so he's actually better than ever. Remember that switching is faster so PT can flexibly shift between his teammates far more effectively than before (it is seriously hard to prevent PT from switching without exposing yourself to constant big risk).
I think you overrate Mario a bit still. Mario is definitely good, but it's not like Marth and G&W are the only two who can zone him. Meta Knight can do it too and quite well, and he has few tools to abuse other characters who have to worry about being zoned out. Like, Mario vs Sonic? This is theory fighter all the way on this one, but on paper it sure looks like this should lean toward Sonic. Mario won't be keeping Sonic out, and I find it hard to see his superior KO options outweighing Sonic's massive speed advantage and the fact that honestly Sonic is gimping Mario more than Mario is gimping Sonic. I definitely am not sold on Mario having overcome natural Ice Climbers problems. A character like him has few options to avoid being grabbed by the duo, especially as he has to overcome well placed walls of Blizzard to even attack their shield in the first place and ice blocks eat fireballs. Now, I'm not saying Mario has particularly bad matchups; he is a character who is probably pretty predictable to not have any truly awful ones. I just find it hard to say that he has only two slight negatives; I would expect to see him have several more. Slight negatives of course, he is definitely good, but I think more negatives than two.
As per the suggestion people are sleeping on R.O.B., that's plausible enough. Unless we screwed something up, his uthrow isn't really that good at killing (the idea is that it kills when R.O.B. can't land anything else but isn't what he wants to have to rely on), and I think you overrate just how much you get out of dthrow (though it is definitely a great throw). The things you're saying about his matchups being externally better anyway is easy to see; intuitively I'd agree with that. I haven't really seen anyone using R.O.B. much though; I'd definitely like to see more of him.