Wow, and I thought I was obsessed with gardening! I love the whole "top floor is a greenhouse" thing...that is freaking brilliant. I would love to see some pictures if you are willing to share.
My sim household is on a relatively small lot so I resorted to a small outdoor garden and pots on the patio for out of season plants. Every season I rotated what was outside vs. what was on the patio to keep things growing year round until I got everything up to perfect.
I also planted a row of tulips and crocus along the front of the house right in front of a decorative (i.e. non-gardening) flower bed, and spliced all of the other flowers onto them (only 1 splice per plant though) to add more color.
I am far too lazy at the moment in my game to work on fishing, so have settled for growfruit and pomegranate for fertilizer with the help of a bee box. Took a while, but I did finally get to all perfect. Only plants I'm missing now are some of the herbs (chamomile and 1 or 2 others). I have the splices for adding them to existing plants, just haven't done it yet.
No need to go through all that trouble for frogs for wolf eels, btw. The best fish are all equally good as fertilizer, none is better than the other, so it is easier just to catch salmon using whatever bait you have readily available. I was ambitious enough to look into the fish-as-fertilizer thing...just never started actually doing it. My sims had twins and just had no time since then. lol