I don't agree with #3. I think if you look carefully at the sonnet, you can see that the comparison is made between the flowers the speaker receives and the love that the speaker has, but the comparison is made between the flowers and the way that this love is expressed by the speaker--in her verse. Note the reference to "thoughts" which are "here unfolded," presumably in the speaker's poetry.
I think that the main comparison being made is between flowers and the love the speaker has for the person being addressed. This is the main metaphor at work in this sonnet.
The speaker is comparing the love she and the other person share to flowers. The other person has brought her flowers -- has loved her. But now her flower bed is overgrown with weeds and needs to be tended so that the flowers (love) can flourish again.
Beloved, thou hast brought me many flowers
Plucked in the garden, all the summer through
And winter, and it seemed as if they grew
In this close room, nor missed the sun and showers,
So, in the like name of that love of ours,
Take back these thoughts which here unfolded too,
And which on warm and cold days I withdrew
From my heart’s ground. Indeed, those beds and bowers
Be overgrown with bitter weeds and rue,
And wait thy weeding; yet here’s eglantine,
Here’s ivy!— take them, as I used to do
Thy flowers, and keep them where they shall not pine.
Instruct thine eyes to keep their colours true,
And tell thy soul, their roots are left in mine.