Bidoof has a later post which doesn't mention the store-bought vs. wild distinction and has been holding true for me so far (I don't think I have more than, say, 5% store-bought flowers at this point):
http://bidoofcrossing.tumblr.com/post/51137777970/animal-crossing-new-leaf-hybrids
I haven't fully tested everything in here, but I'm trying to align to these guidelines now. Previously I had a number of combos that used to be good in Wild World (and, by extension, City Folk) that weren't producing squat. What made me decide that this guide was probably the right way to go was when I had an all-red rose plot spawn a pink rosesomething that
never happened in previous games: