Learn Finnish: Sää oli eilen kylmä, mutta nyt on vain pilvistä. - The weather was cold yesterday, but now it is only cloudy.

In the first clause, the subject is explicitly the noun sää (weather), so the adjective kylmä takes the nominative case. In the second clause, there is no grammatical subject. In these generic, subjectless weather expressions, the adjective describing the condition must be in the partitive case.

How would we change the second clause to say 'but now it might be only cloudy' using saattaa?

You would say mutta nyt saattaa olla vain pilvistä. The epistemic modal verb saattaa takes the third-person singular form since it is a subjectless clause, and the main verb on changes to its first infinitive form, olla.

Why isn't there a word for 'it' in the second clause (nyt on vain pilvistä)?

Unlike English, Finnish does not use dummy pronouns like 'it' to introduce weather conditions or time. You simply use the third-person singular verb (on) all by itself. Adding se here would sound very unnatural to a native speaker.

Does the placement of vain (only) matter here?

Yes, it determines the focus of the sentence. Placed right before pilvistä, it emphasizes that the weather is only cloudy (and not, for example, raining). If you moved it to the beginning of the clause, as in mutta vain nyt on pilvistä, it would mean it is cloudy only now and at no other time.