The Petunia I would use "the", if I were talking about the "species" (plant kind in general)

I like plants shoot. A "plant shoot" is the part of the plant that will "shoot" out of the ground, when the seed "germinates" ("wakes up" and starts pushing upwards through the soil to get to the sun).

It was a long time staying home since gratuate, I can smell decayed gas out of my body, so it was time to get downstairs to have a break. And then, I went to the garden with my camera after rain over. Think that "with" expresses companionship, so that would be reserved for a person!
U never feel that if you weren't here, it was so full of life! It was a wonderful scene that you had to have a look, they were green and they were red, so colorful! Was this "they" refering to the petunia plants and blossoms? 

Petunias (meaning possibly the flowers, as you photographed them!)

I love taking photos of flowers. 

It has been such a long time that I've been staying at home since graduation; I think I was starting to rot (in my room? If this is left out, it is hard for the reader to understand what "downstairs" and "outside" are all about!). It was about time to get myself downstairs and take a break. Right after, I went to the garden, my camera with me ( ;) ), just as the rain was over.

If you weren't there, you simply couldn't have known(standard phrase, "feeling" is implied); the garden was filled with life! (...was so lively! -better probably-) You should have been able to look at this wonderful scene, the green and the red, so colorful!

I hope I didn't stray too much from your initial, intended thoughts?!