I want to begin by stating that I know SE's stance on this as they have been very blunt about it in the past, however as stubborn as a person I am, I wish to raise a pressing issue as to why this is a big problem.
This thread is simply about damage or buffs that do not take effect until after the animation has completed. My first example I am going to bring up is the glaringly obvious ones and in my opinion some of the more crucial ones - PLD..
PLD
Using Hallowed Ground as an example, there are countless times where I have dropped to 2k HP and worried if I was going to get a heal or not, used Hallowed Ground instantly, and still died.
On top of this, all of PLD's defensive skills work in a similar fashion. This makes reaction/twitch tanking impossible, and you have to simply rely on prediction. This makes tanking mechanics even more boring then they already are for a PLD.
Finally this goes for both WAR and PLD, or in fact any interrupt skill. Instead of the true "instant" description, the interrupt is actually scaled on the duration of the animation. This means that the stun is actually about 1 second (give or take) after you hit the button, and this is far from "instant". Having to allow for both latency and the animation delay often means that the line between interrupting a fast casting spell, and not interrupting it is extremely small. It is once again, less about twitch/reaction mechanics and more about prediction - which in turn makes the mechanic dull.
BLM
Now it's arguable that since BLM is pretty much the strongest ranged DPS class at the moment, that they don't really need a "buff", and what I am going to mention here will indeed appear to be a "buff" but hear me out.
Firestarter procs.
This one is probably self explanatory to any BLM out there.. Currently the problem is this-
Depending on the distance you are between the enemy mob, after successively casting Fire 1, the animation overflows the GCD (as the little fireball has to hit the mob) before a Firestarter proc actually shows on your screen. Meanwhile you are already 1/4 of the way through your next Fire 1.
So a BLM has 2 options. To continue casting that Fire 1 and potentially waste a Firestarter proc (if one were to proc on the next Fire), or interrupt the cast and burn the proc, then go back to Fire 1.
Both options mean a loss on damage.
In addition to this, often because of the animation - Swiftcast fails to take effect if you cast immediately after using the skill. This reduces the point of Swiftcast, as you have to interrupt the cast to allow Swiftcast to take effect on the spell. Similar story for Surecast but to be honest, that skill is more useful for healers anyway.
Healers
This one is pretty obvious. Cures are not instant, they go off after the animation is displayed, therefore a healer has to allow for the time it takes to play the animation + cast time + GCD.
Similar story with Stoneskin... If you know a big attack is coming and the tank is at full HP - you have to also allow a 1-2 second buffer after casting the spell for the buff to actually take effect.. So this means you have to begin casting about 5 seconds before the tank gets hit.
Summary
Basically all of this attributes to a sense of lag and clunkyness in overall gameplay. While it does appear that this game is more about looks then it is gameplay, adjusting abilities at the least to apply the buff the instant the cool down goes off would improve the feeling of response, and make the game feel less delayed.
Myself, and I am sure many others can understand weaponskills and other non crucial abilities based on this mechanic where the damage is displayed & dealt after the fireball hits the target, or the polearm stabs them. However in terms of how the gameplay feels - currently it feels slow and laggy.
Simply pushing the buffs / debuffs to the start of the animation would improve the overall feel of gameplay by a huge amount and would reduce a lot of the complaints on game lag.
It feels like you guys tried to do a reaction/twitch style mechanic, but only went half way - and picked aesthetics over the feeling of a fluid battle system. For the most part, the game "looks" nice, but certainly doesn't "feel" nice.