Well, let's assume we're using the three-year game before things wrap up, and a twelve-month cycle. (Shortening it down to four months made things go by quicker, but everything feels humorously quick and absurdly lucreous. I mean, growing a turnip in 3 days and selling it for $1000?)
That gives us a total of nine growing seasons: three spring, three summer, three autumn. If we spend all our time making money on the farm, I'd assume that we should have enough money to buy everything reasonable in the game - all the equipment, all the house upgrades, and so on. That means the income for any one three-month season should be around 1/9th the total cost to purchase everything, roughly.
This can be modified a bit. The first seasons will be less than productive, both for not having the money for the best seeds and not knowing the best produce at the start. On the other hand, you can spend winters mining for gemstones, or perhaps selling baked goods or something for a higher profit. Thus, I would recommend the average seasonal income to be 1/8th of the total for everything, if you are looking at an "easy" game, or perhaps more like 1/10th the total for everything, if you are looking for a "harder" game or one with a lot of optional extras.
In either case, I think it would be best that each season averaged around the same amount of income. That is, Cucumbers, Corn, and Eggplants bring in roughly the same amount of money over a three-month span.
"Friendship" plants sound interesting, and can be useful to more than one pony. Perhaps Fluttershy likes carrots (for Angel) like Carrot Top? Also, there are lots of ponies in ponyville, and so lots of different preferences - perhaps start making a list of what every pony would like? Just because carrots are a "gift" crop doesn't mean they can't be one of the quick-growing crops for autumn, for example.
I'm afraid I'm not a farmer and so don't know what makes a good "spring" crop from a good "autumn" crop. You might want to make the flowers di-seasonal rather than all-seasonal, just for a change. Different Spring-Summer and Summer-Autumn flowers are more interesting than "everything all the time" flowers.
I mention this because if, say, you have time to water all your plants and talk to everyone in ponyville, then Fluttershy's place can be a longer walk from the town. On the other hand, if taking a detour of two or three extra screens can put you an hour or so behind schedule, then you'll want to place Fluttershy's cottage just outside town (and perhaps a "back way" of following the river, to Sweet Apple Acres and your farm).
I'd say a lose condition is if you run out of time before you can get whatever you want.
I think that someone should be able to get the best equipment, get the best house, and become best friends with at least one character through a "normal" playstyle of tend crops - tend animals - visit character - give gifts. A "busy" playstyle would be what someone could reasonably achieve if they spend every day planned out for the shortest time to a visit and the best return for their money. A "lazy" play would be just doing the basic stuff, like buying and growing only the cheapest crops.
How much should they get with the "lazy" playstyle? Should they have the best house, or should they just be scraping out of debt by the end? Perhaps all the best equipment and the 2nd best house? And of course, there is what the "busy" player should be able to accomplish at maximum. I'd assume the best equipment, best house, and best friends with the main cast at least, although I wouldn't assume best friends with the entire town or accessing all the secrets of the game as well.
(And when I say 'best equipment', I'm talking about Mithral Axes and Scythes, or their equilivant.)
Ah well, something to think about.