Late, but here's something to start with while I have the time.
Special thanks to
memoryman3
for giving me just the right example of what NOT to do:
http://www.gamefaqs.com/boards/633202-super-smash-bros-for-wii-u/72646712
I feel like this thread right here is a summary of why people would take issue with Daisy. The way her support is carried out needs improvement.
First thing's first, the beginning sentence. Starting out with an insult towards the other girls does not get you any points. You're insulting characters liked by other fanbases, giving them less reason to take your own opinion seriously. This isn't even limited to just Peach and Rosalina though, this happens with other characters like Waluigi and even Bowser Jr. too. Seriously, don't do that.
The second thing is having any condescending attitude. Treating people who don't think much of Daisy as people who just never played as her feels pretty damn condescending. Now, for a regular jerk like myself, I have no problem carrying that attitude, but I'm a self-admitted jerk. Are you a jerk? Then go ahead and do that if that's how you want to support what you like. Won't do you any good though, I'll guarantee that.
The third thing is forcing statements of objectivity on areas where there's clearly only subjectivity to work with. Saying that Daisy IS more fun than others is objectivity where there should be subjectivity. Wording is key. Saying something like "oh, she adds so and so" is better, since you can argue that you're right about whatever unique value you're promoting while avoiding a clash of opinions argument. Saying how you personally feel is easy to do, but wording that into a way that tells everyone why it's good to have in general is much more effective. Try to do this without saying something stupid though. I'd recommend not even mentioning Peach or Rosalina because chances are you'll just cause an argument of a different variety to start by doing so.
Now, with that out of the way, I can cover why other fandoms have it easier. It's mostly due to the characters themselves just being better off. K. Rool's fandom wouldn't see as much hate because he had the role of a main villain for so many years. Isaac is the protagonist of Golden Sun so it's hard to be more noteworthy than he is in regards to his own franchise. Daisy had a role that was already done by two other females for her debut, and for every appearance after she took on a Luigi/Waluigi sort of role. Luigi gets by due to getting things like the Mansion games and New Super Luigi U coming his way while Waluigi... eh, I'm not really sure about him. I feel like he gets hate too, but that's more so within the Mario fandom than within Smash. Within Smash I think he gets by because he lends himself well to memes, and Smash fans love their memes no matter how unfunny they are. It's petty but what can you do? This isn't a problem with the fandom necessarily but it's something that does stand in the way and separate Daisy from others (not to her benefit, obviously).
The other thing is to just maintain some damn self-control.
Like this little discussion. Seriously, I don't wanna come off as too hostile due to the irony it'd cause, but the Daisy fandom honestly strikes me as one of the more hostile ones out there at times due to moments like this. Stuff like this, or "b-b-but Rosalina!!!" when someone calls Daisy a recolor, or spamming Peach's miiverse with "vote 4 Daisy!", or attacking Waluigi because he got into Super Mario Maker while she didn't, any of that garbage is enough to actively warp a person's viewpoint of a character and make them outright hate them. I could go on and on about this but I feel like I'd just cause drama if I did, so I'll leave this at that.
I feel like I have more I could say but this is what I have in mind for now. Take it or leave it, this is what a bystander who (mostly) already has what he cares for in the game has to say.
Also, I just realized that I worded this like a list of things to note do instead of just a list of problems, but I think it works like this.