I think it's a difficult situation. It's true, playing against a farm deck isn't fun, but is it fun against the AI when it's a biting deck? I don't think it is very much. To the contrary, I'm more annoyed when I play t50 and it's not a farm deck, since I play t50 for farming purposes solely. If I want to have fun, I'd rather play the people in t50, not an AI that poorly plays their decks.
Without farm decks, it might take ages to win specific rare cards needed for, say, an fg farming deck. Maybe it should take ages to acquire these rare cards, but they are essential for a lot of effective decks. Farming just isn't that fun in general, but it would be miserably slower if t50 didn't have farm decks. I talked to a player the other day who was depressed because it took him so long farming level 3 and pvp just to upgrade one card. I suggested he try farming FGs, but he lacked the eternity for ScaredGirl's, the electrocutors for rol/hope, the pulvs for the no CC deck, etc. I told him not to worry about it because of the farm decks on T50.
It might mitigate the situation if rares could be purchased for, say, 20,000 electrum. Then at least players won't have to feel hopelessly relying on luck to win the eternity needed, for, say, ScaredGirl's fg farming deck. Hopefully they'll win the specific rare sooner than that, but if they can't, at least there's a backup to which they can steadily progress. It'll be an expensive goal, but at least it won't seem hopeless.
The AI in general isn't very fun IMO. There are so many ways to exploit it, and FG killing decks are generally designed to do just that for many of their strategies. Did the AI play a pulverizer a turn before you could? No problem, play an hourglass and a pulverizer and he'll pulverize the hourglass and you can destroy his pulv. Have an FFQ against AI with creature control but no quintessence handy? No problem, just use antimatter on it. The AI has gotten a lot smarter since the game was introduced but it's still pretty dumb: mutating one of your creatures that aren't a major threat when you are rainbow into something much better, etc.
The real fun is in playing real people. I think everything else is just a grind, and it's already quite slow as it is. I'm quite thankful for the farm decks and think it speeds up the boredom that is already involved playing t50 decks against the AI. T50 decks also are especially prone to be poorly played by the AI. For instance, amassing fire quantums before using fire lance just doesn't register with the AI. A lot of these decks require specific strategies and sometimes heavy brainpower, and the computer just doesn't do very interesting things with those decks. Even the decks not made for farming at all can be ridiculously easy to beat and boring just because the computer doesn't know what to do with it: generally the more sophisticated the deck, the worse the AI does with it.
If we really want to make it challenging to win rares and based more on perseverance and skill than luck, perhaps rares should only be obtainable through pvp and false gods who at least have the extra hp, 3x mark, and extra draw to make up for their poor AI. For a truly elitist game we could have a system where a pvp win grants the winner the loser's card and the loser loses the card from his deck. Then it would really be the top players that have the rare cards only as bad players would not be able to win them and, even if they could, they wouldn't be able to hold onto them for long. That would also make the rares truly hard to get and keep, so people wouldn't design so many decks around rare cards.