First, general comments:
- Overall, this could be made more powerful if shortened quite a bit. I think the implementation of your good idea has suffered a bit by attempting to put it into sonnet form. At present, I don't think there's enough content for the fourteen lines required. Also, titling it as a sonnet sets up an expectation regarding meter, rhyme scheme, etc. that this doesn't meet. I'd suggest compact free verse.
- The metaphor of a flower could be made to work here, but needs some adjustment. However, since flowers are so often employed as metaphors (or similes) for love or friendship, accomplishing that without sounding cliched is a tall order.
- Changing the poem to address your friend rather than speaking generically may make the piece more powerful by more effectively bringing the reader in to vicariously share the emotion. E.g., "You were a flower, unnoticed in bloom." (I'm not suggesting those words, just illustrating.)
Here are a few more specific suggestions:
A good friend is like a flower-
Hardly, if ever, noticed in bloom,
Is this true? It would probably be more accurate to say, "sometimes, unnoticed in bloom."
Whose loss aches each crevice
"Crevice" doesn't work well for me here. (The heart has crevices? What does it mean for individual crevices of the heart to ache? Also, the word crevice normally connotes something hard, like stone.
Of the heart, once gone,
Leaving his lingering fragrance behind.
Consider whether everything so far could be compressed into one terse, multi-line sentence and, as I said above, I'd consider free verse.
When together, in joyous times,
He multiplies twicefold our smile-
Like a faithful mirror;
I'd dispense with the mirror simile in the middle. Although it expresses a unique idea, I think it would be better to build on the flower image throughout.
But when one is bereft of friends-
Not differing from a withered stem
Albeit fine and sturdy, lacking leaves-
This might be more powerful if said in the first person ("Now, I am a stem, fine and sturdy, but lacking leaves). Also, instead of "friends," you might consider extending the metaphor by using some characteristic of the flower ("bereft of your radiance."). Also since you're now using the flower to describe yourself, you probably need some cleverness here make the switch without making the metaphor inconsistent. (Perhaps consider, keeping your friend as the flower bloom, and make the lonely stem represent the place your friend formerly occupied).
And loneliness and sadness take over,
There is no end to which loss cannot reach,
And ache till death separates them fully.
These last three lines are a bit too "telly." By enhancing the "lonely stem" metaphor I think you could illustrate what this says in a way that's more poignant.
Though I'm
far from being an expert poet, I hope these suggestions are helpful. :-)