When you ask "What is the most important theme in Sonnet II?" you imply that there are more themes than one. I suppose a sonnet can be read and understood in this light. I suppose that then the response might that the themes are what happens to "beauty's field" and "youth's livery" after "forty winters," that’s forty more winters; that beauty lives on in the eyes of the beloved ("within thine own deep sunken eyes,"); and immortality is in the life of a child successor (“This were to be new made when thou art old,”).
However, the way sonnets are structured, this approach misses the mark of the intent of a sonnet. Sonnets are a very formulaic genre of poem. There are several structural forms stemming from the original Petrarchan sonnet form, developed by Italian poet Petrarch. Edmund Spenser and others adapted the form, which led to the Shakespearean form (or English sonnet form), presently under consideration.
Shakespeare's sonnets are structured as three quatrains (twelve lines of abab cdcd efef rhyme: a quatrain is four lines of abab rhyme) followed by a couplet in a cc rhyme. The 5th and 9th lines pivot or turn the topic being address. The pivot of the 9th line is called the volta and introduces the resolution to the problem spoken of in the first two quatrains (lines 1-8). The ending rhyming couplet wraps the sonnet up with a triumphant or glorious etc finish.
In Sonnet II, the topic introduced in the first quatrain is the image of beauty devoured by time ("forty winters"). These four lines are an introductory adverbial when-clause that sets up the topic to be thought about: "When forty winters shall besiege thy brow, / ... / Thy youth's proud livery ... / Will be a tottered weed ...." Line 5 pivots and advances forty years in the future to speak of when "being asked where all thy beauty lies." Lines 7 and 8 present the problem: it "would be a shame" if at that time the only answer to the question "Where does all thy beauty lie?" were "within thine own deep sunken eyes," in other word, the speaker's own aged and "tottered" eyes.
Line 9, the beginning of the third quatrain, presents the volta that introduces the resolution to the problem shown in the second quatrain (5-8). The solution in the third quatrain (9-12) suggests that were the beloved to parent a child, that beauty, which in forty years hence will be "besieged," will still live on in that grown child. The sonnet’s ending couple (13-14) wraps up eloquently by saying that his beloved will be renewed despite the cold blood of age by seeing the warm blood flow in that other’s youthful life.
When Sonnet II is examined in light of its structure, it seems reasonable to say that the one pervading theme, presented from three perspectives or from three different aspects of the same topic, is the redeeming joy of sustaining youth by passing it on through parenthood. Incidentally there is debate about how the Shakespearean sonnet structure should be described with some prefer to analyze it more akin to the Petrarchan original by describing it as having two quatrains followed by one sestet (six lines in an ababcc rhyme scheme: a quatrain plus ending couplet).