El deseo cambió con el tiempo.

Because deseo is the subject of the sentence, and Spanish often uses the definite article with nouns, including abstract nouns like deseo.

Here, el deseo means something like the desire or desire as a known idea in context.

If you remove el, the sentence sounds less natural in most normal contexts. Spanish uses articles more often than English does.

Here it is a noun.

You can tell because it comes after el, so el deseo means the desire.

But deseo can also be a verb form in another sentence:

• Deseo ayudarte. = I want / desire to help you.

So the word deseo can be either:

• a noun: desire
• a verb: I desire / I want

In this sentence, it is clearly a noun.

Cambió is the third-person singular preterite form of cambiar.

It matches el deseo, which is singular:

• el deseo cambió = the desire changed

The preterite is used because the sentence presents the change as a completed event in the past.

Compare:

• cambió = changed
• cambiaba = was changing / used to change
• ha cambiado = has changed

So cambió is the natural choice if you are simply stating that the change happened.

The accent mark shows where the stress goes: cam-bió.

Without the accent, cambio is a different word:

• cambio = I change or change as a noun
• cambió = he/she/it changed

So the accent is important both for pronunciation and for meaning.

A simple pronunciation guide would be:

el de-SE-o cam-BYÓ con el TYEM-po

A few notes:

• deseo has three syllables: de-se-o
• cambió is stressed on the last syllable
• tiempo has a diphthong: tyem-po

In standard Peninsular Spanish pronunciation:

• c in cambió is a hard k sound
• b is a soft Spanish b/v sound
• tiempo sounds roughly like TYEM-po

Literally, it means with time, but in natural English it usually means:

• over time
• as time went by
• in the course of time

It is a very common Spanish expression.

A close alternative is:

• con el paso del tiempo = with the passing of time / as time went by

That version is a bit more explicit and sometimes slightly more formal.

Here it means time.

It is true that tiempo can mean both time and weather in Spanish, but context usually makes it clear.

For example:

• No tengo tiempo. = I don't have time.
• Hace buen tiempo. = The weather is good.

In con el tiempo, it definitely means time.

Yes, you could.

The difference is mainly about how you view the past action:

• El deseo cambió con el tiempo
  = presents the change as a past fact

• El deseo ha cambiado con el tiempo
  = presents the change as something that has happened and is relevant now

In Spain, the present perfect (ha cambiado) is used quite a lot, especially when the speaker feels the past is connected to the present. But in a sentence like this, the preterite (cambió) is also very natural.

Yes.

The neutral order is:

• El deseo cambió con el tiempo.

But you could also say:

• Con el tiempo, el deseo cambió.

That version puts more emphasis on with time / over time.

Spanish word order is more flexible than English word order, although not completely free. In this case, both versions are correct.

Yes. Cambiar can be used in more than one way.

Here it is intransitive:

• El deseo cambió. = The desire changed.

But it can also be transitive, with a direct object:

• El tiempo cambió su actitud. = Time changed his attitude.

So in your sentence, the desire itself is what changed. Nothing is being directly changed by a person or thing in the grammar of the sentence.