1. With "skills tree", if you mean being able to choose something different from another player of the same job, they were a bit more choices in the past. And they were removed because everyone were taking the same most useful and optimised thing, making the rest useless to have in the game. Most of other mmos with "choices" are having this problem too. For example when i was playing GW2 there was a lot of people who did tell me "why did you choose these skills ? Go copy/paste this build from metabattle, nodody is playing with what you are using", when i did choose some things for fun rather than conforming to the META. There is still a bit of fake "choices" in FF14 as well : if you jump into the latest savage raids with your tank, don't do it with tenacity melds if you don't want some people harshly telling you that crit/dh/det is better.

3. I think this is fine because unlike other crafting classes, cooking doesn't require intermediate ingredients from other classes all the time. For example if i want to do some armor, i will often need some leather or jewels i can't do with the armorer, wich makes the item more lengthy and difficult to do. If you lower the ingredients required for culinarian recipes, they will become way too easy to do compared to other crafting classes... and people will probably start asking to nerf them as well for the sake of making everything balanced. As if crafting was not dumbed down enough already.

3. Yes, another 3. Needing a lot of ingredients is realistic. Did you never get baited by some "do this delicious recipe with eggs and milk only !" Youtube thumbnails, to realise once watching the whole video that on top of the "only" two advertised ingredients, you also need this one, and this one, and this other one too ? XD