The one thing I hate about the current system is the fact that cooking plants does not return seeds. It sounds trivial, but it isn't. It means that if I let my legendary cook go for a couple of minutes he'll turn all my plump helmets into roasts (which is good) but leave me absolutely no seeds. None. At. All. He'll also get rid of any booze in the fort, which just makes problems later when my dwarves are forced to view the world without the benefit of alcohol. So the only thing I let the idiot cook is meat. And only once its dead. The only solution to this is switch the cooking job off and on every few minutes and manually monitor the seed/farm plot levels, which gets tres annoying.
The other major problem with this is that it is
completely unintuitive to new players. There is absolutely no indication anywhere in the game that your dwarves won't save seeds if you cook your plants, and no reason that a new player would know this if they hadn't seen the wiki. The fact that it defaults to cooking all those things (even though it's usually a terrible idea to do so) makes things even worse.
As far as cooking booze goes, it's planned to change when cooking is done in a more detailed fashion. I wouldn't really call it an exploit, though -- it's not actually a
good idea for an established fortress to cook booze. I never do it, not because I view it as cheating but because, generally, keeping full supplies of food is much easier than keeping full supplies of booze -- turning booze to food is a bad decision, no matter how good the exchange rate looks. It's much better to make food from processed plants.
Y'know, you could farm something other than Plump Helmets and still get seeds and food, without cooking booze.
You can, yes, and many players do farm things other than Plump Helmets. But the only reason to plant something other than Plump Helmet is to make things harder on yourself. Other ways to "self-nerf" your food production at least have some legitimate (if contrived) reason (e.g. choosing Dwarven Sugar over Syrup at least lets you save barrels).
This is untrue. There are many, many reasons not to rely on plump helmets. You already mentioned one (barrels). Dividing your food and drink chains is another -- if you don't divide them, even a slight hiccup in your booze supply line (say, because you run out of barrels) will almost
instantly make you run out of beer as your cooks use it all up. This can be a huge problem, and it's easily avoided by taking a few seconds to set up additional farms + workshops.
Second, dwarves get happy thoughts for eating food they like. They get unhappy thoughts for having only one kind of booze. You will get much, much happier dwarves in general if you produce a wide variety of food.
Third, plump helmets have a catastrophically low drink value (2), and will therefore cook into horribly low-value roasts. Compare this to Quarry Bush Leaves (5), or sweet pods (20!). These values contribute to the happiness of your dwarves -- your
entire fortress will be more happy, and therefore less prone to tantrums and tantrum-spirals, if you use better food. Sure, you can grow plump helmets slightly faster -- but that doesn't matter. Your dwarves will still eat the same amount. If they eat a Quarry Bush roast they'll be slightly happier. If they eat a Dwarven Syrup Roast they'll be ecstatic.
A fortress that makes extensive use of sweet pods and quarry bush leaves can easily buy out an entire caravan with a single masterwork roast. A fortress that only makes plump helmets will be less happy (because you're feeding them terrible food), and won't have nearly as much value for trading or attracting immigrants.
Plump helmets are not bad as an emergency stock, but mostly they're good for newbies, because they're quick and easy. (Well, that and they're the only edible indoor plant you can grow in the winter, making it logical to switch all your farms to them at that point.) In the long run, other plants have the advantage over them other ways.