I think if you breed by color the value of the smaller frog needs to be higher then 50% of the cost to breed or your coins go down too fast.
Also I'm thinking of playing every other day or every two days as soon as I finish dexting all the lower level frogs.
That said I try to focus on breeding frogs with at least a 2 out of 4 chance of adding a new frog to the Dex. if I Dex by breed then every body color has one 25% frog and then there are the stuborn frogs that won't breed. I think the best way to deal with those is to mix up the combos, try another frog rather than breed 8 or more of the same frog. So, my vote, is to breed by color, working my way up the Dex breeding frogs of similar cost.
I've got 25 of the new frogs, %) damn starting to get crowded :P