Я хочу чай, а не кофе.

They are functioning as the objects of хочу. In modern Russian, that usually means the accusative.

For this sentence:

• чай is masculine inanimate, so its accusative singular looks the same as the nominative: чай
• кофе is an indeclinable noun, so it also stays кофе

So even though both words look unchanged, they still fit the grammar of the sentence.

Yes. Чая is the genitive form, and with хотеть it often gives the sense of some tea or an amount of tea, rather than tea in a very general or categorical way.

So:

• Я хочу чай = straightforward, neutral
• Я хочу чая = often sounds a bit more like I want some tea

Both are common and correct.

In Russian, а is very often used for contrast or correction. The pattern X, а не Y is a very common way to say X, not Y.

So Я хочу чай, а не кофе means you are contrasting one choice with another.
Using но here would sound less natural, because но is more like but, not this specific kind of contrastive correction.

Russian does not have articles. There is no direct equivalent of English a or the.

So чай can mean:

• tea
• a tea
• the tea

The exact meaning depends on context. If Russian needs to be more specific, it usually uses word order, context, or words like этот meaning this.

Кофе is a borrowed noun that is usually indeclinable, so its form does not change across cases in standard usage.

Traditionally, кофе is treated as masculine in careful standard Russian:

• горячий кофе
• вкусный кофе

You may hear neuter agreement in casual speech, but learners are usually taught to use masculine.

Yes, often you can. Хочу already shows I want, so Хочу чай, а не кофе is perfectly natural, especially in conversation.

Including я is also normal. It can make the sentence a little clearer, fuller, or more emphatic.

Yes. Russian word order is flexible, and changing it changes the emphasis more than the basic meaning.

For example:

• Я хочу чай, а не кофе. = neutral
• Чай я хочу, а не кофе. = stronger emphasis on tea
• Я чай хочу, а не кофе. = more conversational or emphatic

So the original version is the most neutral, but other orders are possible.

Because а is a coordinating conjunction introducing contrast, Russian normally puts a comma before it. This is standard punctuation in sentences like X, а не Y.

So the comma in Я хочу чай, а не кофе is expected.

The stress is:

Я хочу́ чай, а не ко́фе.

The main stress points are:

• хочу́ — stress on the last syllable
• ко́фе — stress on the first syllable

A rough English-friendly pronunciation would be:

ya kha-CHOO chai, a nye KO-fye

That is only approximate, but it helps with the stress pattern.

No. In the present tense, хочу is the same for both men and women.

Gender would appear in forms like:

• я хотел = I wanted / I would like (male speaker)
• я хотела = I wanted / I would like (female speaker)

But in я хочу, there is no gender difference.

It is understandable, but it can sound a bit direct depending on the situation. For a more polite request, Russian often uses forms like:

• Мне, пожалуйста, чай, а не кофе.
• Я бы хотел чай, а не кофе. for a male speaker
• Я бы хотела чай, а не кофе. for a female speaker

So Я хочу чай, а не кофе is grammatically fine, but not always the most polite choice for a service situation.