Hello. In first: don't forget that when you write a question in Spanish you should put two signs for asking: ¿ ... ? That's frequently mistake from English students. About your sentences: Informal way (naturally speak) : ¿Qué quiere desayunar? Formal way (in restaurants or hotels): ¿Qué desea desayunar? ¿Qué gusta desayunar? ¿Qué gustaría comer para el desayuno? The key to difference informal than formal way is what word use to ask. For example, in formal context the word "desear" (wish) is better to "querer" (want). It's not necessary that you explicit the pronoun "usted". In general, when you use Spanish language the pronouns are implicit.

Both sentences are possible, grammatically correct, though I would made two minor changes, I would change the preposition and remove "por favor" in the end. ¿Qué quiere comer al desayuno? (formal) ¿Qué quieres comer al desayuno? (informal) You can also say ¿Qué quiere desayunar? (formal) ¿Qué quieres desayunar? (informal) If you want to use the preposition "para", then you can say: ¿Qué quiere para el desayuno? (formal) ¿Qué quieres para el desayuno? (informal) All those sentences are in present, You can also use conditional tense: ¿Qué quisiera desayunar? (what would you like to breakfast?) (It is unusual to use this word as a verb in English, but it is also possible). ¿Qué quisieras desayunar? (informal) I hope this helps you.

yo diría: Formal: ¿Que desea usted desayunar? Informal: ¿Que quieres desayunar?