Well, you clearly already know that being polite is vital, so I don't need to say that!
As for other advice, make sure to keep it concise, reasonable, and on-point - simply saying that you saw the press coverage of the game and are wondering why your favourite character is absent will make the point very clearly. There's no need to write a large number of pages, or even more than a couple of short paragraphs, in a letter to make the feedback understood.
Don't be accusatory or point fingers at the company or individuals within it (for example, whilst I may speculate about the rumours of Miyamoto-bias on a fan community like this, it has
absolutely no place in a complaint/feedback letter). You do not want to risk sounding like you're ranting, even if that's not the intent.
It is absolutely fine to briefly express disappointment that, for example, an inanimate object like a Mahjong tile was included instead, but that's as far as that should go - as everyone knows,
bashing other characters just because one doesn't agree with them is poor form. (For balance: As strange a choice as it is, the Mahjong tile is a reference to
an early Famicom game that helped the system's success in the days before Super Mario Bros. was released.)
After stating your case, it would be best to end on a positive note, by stating that you enjoy the games that Daisy does appear in, and that you hope to see her appear in more games - such as a main series platformer or whatever you prefer - in the future. Even if you're sending a letter about something disappointing, there's no need to end it on a sour note, after all!
Ideally, you should be able to keep the whole thing shorter than this advice, and your point will be well-understood.
It could be parts of all of these, plus the fact that, for whatever reason, aside from Super Mario Land, they stopped putting her into mainline games.
I've never understood that, especially not when they used to push her so much in major licensed products like Super Mario Bros.: The Movie (yes,
it was a disaster thanks to how the licensees handled it, but it was a major product nonetheless, and it did have traces of things that are true in game canon, the most notable of which is Daisy's relationship with Luigi), and that Super Mario Land pop song that was actually a very big seller back in its day.
I mean, they still include her in almost all of the popular spin-offs and in merchandise lines, but a main game appearance, like her debut, would certainly help a lot!