EDIT: The below mostly applies to the Melee scene, I don't pay attention of the Smash 4 fanbase as much because I want to continue to enjoy the game
The reason that Smash is seen negatively in the FGC is easy: the fanbase. i'll state up front, no I don't fully include you in this Tasty...I also enjoy watching Smash 4 matches (not Melee). But it's true. The Smash fanbase mentality is 100% the opposite of the FGC. A lot of this comes from Smash previously being excluded from FGC events. They were mocked/excluded/forced to play with items in FGC events (including EVO) and eventually gave up and decided to make their own events and scene. And they were good at it, eventually getting into MLG events and on television with Smash. Smash went the full eSports route like COD/Halo/CS/etc. However eventually they were dropped from MLG as MLG moved on to newer games (next version of COD/Halo/Gears) and Smash players refused to upgrade beyond Melee (yes, Brawl was bad. But they were still left behind by MLG for not moving to the next game).
So now the Smash fanbase mentality is focused more around an obsession with eSports and being eSports and how big they WERE. So every move the scene makes is intended to either flex that muscle or prove that they still matter. This is seen from them making demands that seem absurd to FGC events. Stuff like running the entire long ass tournament 3/5 matches, seeding their "Gods" out of pools, having extremely long warmups and VIP areas for the "Gods". This is because they are used to being the big dogs at events run 100% for and by their own people. But the FGC doesn't respect "Gods" like Smash does. So Smashers are mocked and mistreated in their eyes. To be honest the Smash idea of "Gods" is very much an eSports thing. eSports like Dota/LoL/etc are more about spectating the "best of the best" rather than trying to be the best yourself. Most Smash players will actually give up before the match starts when they have to play a "God", which then reinforces that these players are untouchable and they have the final word on all things Smash. This is especially the case in Melee. If a "God"speaks something about the game, it is taken as gospel. In the FGC, if you play a top player your number one goal is to beat and (if possible) embarrass them while you do it.
This turned a little rambling and probably more than a little autistic but it's what I've learned talking to local friends that are a "big deal" in the Smash scene about this exact subject. The Smash and FGC mentalities are just oil and water, but the Smash scene also is much more interested in paying money to attend events and such so the FGC events will keep them around for the paycheck as long as possible. This works well for the Smash scene as well because they can then brag about what a big deal they are being on the main stage of EVO/CEO/etc.
And then of course there's the "they don't shower", "they are all 12 years old", "they are whiny babies", or whatever other spewed by the FGC too. But honestly that applies to both sides and is just a shorthand to mock the general behavior and mindset of the Smash scene.