The biggest thing Splatoon has going for it at the moment is that it's the first time in a long time that Nintendo has pushed a brand new first party IP. (That's not an obscure eshop title, anyway) Don't get me wrong it looks damn good; fresh, inventive, yet classically Nintendo. But it is its status as a brand new franchise that's getting the most attention.

However, with Nintendo's obsession with transplanting their popular characters into other franchises, I have a feeling that sooner or later, stuff like being able to play as Mario with FLUDD will infect Splatoon. And guess what everyone's favourite skin to use online will become? 

Before you know it, Splatoon will have become Mario Paintball, and its greatest asset, its freshness, will be jettisoned like a ued syringe.

This is their chance to show they're not just an old IP factory, but it will slip through their fingers if they shoehorn overused characters into it.

I hope I'm wrong, but if it happens, I called it.

They could add character based skins in future updates or dlc packs.I see no problem in this.It would help boost the game's sales too.I can't find an issue with that.It's not the charachters who give it this freshness you mention but the general concept behind it.

LOL I love how a DLC skin can apparently ruin a game =P

I doubt it, Mario isn't a squid.

Not yet he aint =P
Im sure they can make him a Blooper when he transforms and use FLUDD, the game was made for this.

but maybe he is?

your whole life is a lie. 

Putting Mario in it would effectively make it just another Mario spinoff.

This damages its ability to show that Nintendo can still produce fresh new IPs.

Nintendo has a really weird thought process. Miyamoto himself said this in an interview with EDGE:

"There were heated debates over who the main player character should be. Whether it should be Mario, or a squid."

First of all, the debate was between Mario OR a squid. The designers understood that to make Mario the player character would rule out squids. There is no mention of making Mario a squid for the purposes of this game. Then --

"But at the same time, we had some worries. If it were Mario, we wouldn't be able to create any new IP."

Here Miyamoto says one of the reasons they axed the Mario idea was to make the game a new IP purely for the sake of making a new IP. That doesn't sound like the sort of logic that would result in him saying never mind slap Mario on it anyway. That would be a complete reversal of position.

For once I agree with you.

I can see them doing it, and I can see it shitting all over something that seems good enough to stand on it's own two feet.

More likely than player characters though, I can see them throwing in iconic Mario maps.

Sorry, I didnt realise Mario Kart 8 was a Zelda game or that Fatal Frame V is the latest game in the Dead or Alive franchise =P

Nobody thinks this way, it makes no sense. If Mario was featured in the game from day 1, on the cover of the game and advertised as being in it then sure I would get the complaint. But if he is just DLC awhile on nobody (that isnt trolling) is going to question the success or failure of it because of Mario DLC. Its achievements are its alone, not the Mario IP's