Lots of questions!

I haven't been trying to breed "sets" there just aren't enough pots in the greenhouse to do that right, plus the fact that unlike Fish Tycoon, once a plant has produced seeds, it can't do so again (but can pollinate others.)

I think that whatever system is used, it depends on your goals. Are you only trying to find the Magic Plants? Getting every type of species? Have complete breeding charts that you create yourself? How important is it to have everything in one game vs. finding all of the information across several games?

When I first started, I was interested in both creating my own breeding charts as well as finding the Magic Plants. I worked mostly from two separate games and let the breeding be mostly random (but looking for new crosses I could make) and filling in my flowers and foliage charts from both games. (I would fill in both ways of doing the cross at once, but make the one I didn't do in italics. That way I could verify it if I made the same cross later.) I also started an "all species" chart that I would fill in from either game.

When I completed most of the breeding crosses, I also specifically looked for a full plant cross that I haven't discovered yet. That way I may have started a new track of breeding, or found a new Magic Plant!

Eventually, I also did mutation research and bought new seeds to fill in more holes.

Right now my games are aiming to see how to make the Magic Plants most efficiently, so those games are ignoring many plants that I could make.

Deciding which seeds to keep are the hardest part! There isn't enough room in the seed boxes! I try to keep pairs of everything until there is no more room, then I try to keep samples of each seed as well as making sure that I also have a sample of each flower the seed will produce (that part is harder.)

But I'll (from now on) always try to keep a couple of reptans and ball cacti around since those seem to be the hardest to find again.