Learn English – Why are “indemnify” and “condemn” spelled differently

As Greg Lee and Peter Shor mention in the comments, the "shortness" of the first vowel in natural /ˈnætʃ(ə)rəl/ can be explained by the concept of "trisyllabic laxing": a stressed vowel in the third-to-last syllable of a Latinate word is often given its short pronunciation even if it is only followed by a single consonant. This also affects the pronunciation of the adjectives national (related to the noun nation) and rational (related to the noun ration).

The pronunciation of nature as /ˈneɪtʃə(r)/ with a long vowel is actually irregular; most of the time, vowels in Latinate words are shortened before a "u" in an (orthographically) open syllable, as Peter Shor suggests in another comment (consider tenure, figure, stature, spicule, ferule). I don't know if there are any details about the history of this word that would explain why it does not rhyme with stature or mature.

Interesting question! Here's what the OED has to say about -ious:

a compound suffix, consisting of the suffix -ous, added to an i which is part of another suffix, repr. Latin -iōsus, French -ieux, with sense ‘characterized by, full of’. ... by false analogy in cūriōsus curious (from cūra): see -ous suffix.

and, re: -ous:

Nouns of quality from adjectives in -ous (however derived), are regularly formed in -ousness , ... a considerable number of those from Latin -ōsus have forms in -osity , as curiosity ... see -osity suffix.

and, re: -osity:

The direct reflex of Latin -ōsitāt- in Old French was -ouseté , which is found in Middle English as -ouste , forming nouns from adjectives in -ous suffix... . Loanwords of this period having the latter termination and remaining in use were subsequently re-formed with -osity (e.g. contrariosity n., curiosity n.: compare also religiousty n., voluptuousty n. with religiosity n., voluptuosity n. (all first attested in late Middle English), and hidousty n. with the much later formation hideosity n.). ...