Something being doable doesn't mean it should be patched out.
If someone is able to pull of that Greninja combo in the middle of an actual match, then they bloody deserve that KO, as it would take some memorisation, skill, and reading ability to pull that off.
I'm less concerned about the Greninja combo because, I agree, that takes real skill.
The problem with LM's combo is that, even if it's difficult to perform on lighter characters, it's still too easy to do on heavier characters and that leads to him being a cheese counterpick against heavier characters (who have enough going against them already).
The D3 combo also needs enough stage to work and D3 needs to be at a certain % already. In LM's combo, just land one Nair, get the footstool, then you're golden.
I think that, since balance patches are being applied this time out, any 0-death combos should likewise be removed when they're discovered, and LM's is certainly that.
Cheese counterpicks are what made most of the roster in Brawl unplayable, such as D3's infinite chaingrab on 5 characters, and Marth's infinite on Ness/Lucas. No one is going to want to spend literally YEARS practicing a character that gets destroyed by the opponent counterpicking a character that can infinite them.