Ok, so this thread has been here for a while.
I've addressed your critizism in the last update where I've reduced the time it takes to cook most recipes.
I've been hesitant to explain because I think it's in the spirit of the game to discover its mechanics on your own. Something I am trying to preserve in my mod.

But for people that want clarification I'll explain it here.
For the rest this is a SPOILER:

When you say that you "could take a few ingredients and get a meal that could last someone several days", I agree, but that was something I personally disliked.The problems I saw were
A) You can too easily produce an overabundance of food,
B) especially once your cook gets a high skill
C) The sandwich was the single best food item in every aspect.
D) This also made anything besides grain and meat largely irrelevant.
E) You set up your cooking workshops once and then forget them.

The changes I made are to address these problems:
A) I've increased food consumption
A) +B) I removed quality from food to lessen the impact of a skilled cook.
C) food items with the same number of ingredients now give the same food value
D) For better food you need to produce several different types of ingredients,
this makes more of them relevant but leaves the choice to you.
E) The intermediate products and extra ingredients add a logistical challange.
E) The different levels of food make you change your setup as you progress:
You start off making light meals such as fruit salad and bread.
Once your farms/pastures start producing reliably you switch to making meals,
where the ones that use three base ingredients are the most efficient.
If you produce overhead in the late game, you can mix in the less efficient large meals
for your important gnomes so they take less brakes.
The most complex recipe, the torte, is the only food item with quality
and is a valuable trade good

I agree 100% with your assessments of all 5 problems. Removing quality for anything that can be made into something else keeps you from getting 100 different versions of something with slightly different values. And yeah, reducing the cook time would for the most part solve everything I was annoyed with.