While i can understand where you are coming from, I have to say i disagree with almost everything you claim to be an "issue".
Chocobo Dye: Unfortunately you really scream "I want this without working for it at all" vibe on this. Chocobo Dyeing is great for lots of people never knowing what they might get. I was hoping for a Red or Black, but go Othard blue and turns out i really like the color with certain gear. Without the RNG factor to this i never would have discovered this. Its fun to me and lots of others to experiment and look at all the different options that are available. Plus it also gives those that garden more and more to use the plots for.
Glamour: In any other MMO or game that you play, glamour is purely 100% optional. It is only existant for the purpose of "cosplay" so to speak. It adds a deeper personal connection to your character and for some glamour, its going to cost more. My advice to you is to not go for the stuff that costs an arm and a leg atm. There are hundreds of combinations that you may actually like more. And just as fashion in the real world changes, so does it change in the game. I prefer having to work for glamour as it gives me the sense of "i worked hard for this and not everyone else has it"
Atma: This i can agree on. It really was dumb of SE to put PURELY RNG mechanics on this. Dont even try to argue the "multiple fates = better drop rate". That statement is tired and worn out from the abuse. It would have been better for them to add some sort of progressive element into the fates rather than just 1% drop rate and have at it.
Animus: 1000000000 times better than Atma. Perfect the way it is. ONLY thing that requires any RNG is FATE pops. But that you can also accelerate by finishing fates in the area.
Novus: Again, 10000000 times better than Atma. Its better than a weapon that takes 3 weeks to get, if you spec it right.
All the atma/animus/novus are supposed to take time and work to accomplish. The only part they failed miserably on was Atma. That way its not just another case of "everyone has it".
There will always be the try-hards and "no-lifers". And as far as i can see SE is doing a great job of making people work for the stuff that they dont NEED while still keeping people playing all week.