Two points.
(1) Instant-use abilities should apply their effects immediately. Games have to prioritize functionality over realism when there's a distinct clash between the two. Could you imagine if a first-person shooter was released where clicking the mouse button meant a quarter-second delay for your character to pull a trigger? Indeed, FFXIV already prioritizes functionality over realism in other areas, which is why in a boss fight, whether or not you get hit by AoE is dependent upon where you are when the cast finishes - not when the animation goes off.
(2) The Benediction issue (and others) are due to how SE designed their netcode. When a client machine and the server aren't in sync, the server-side state is the trusted one. This isn't typically the case in online games, particularly where PvE is concerned. I don't know if you've played Guild Wars 2, for example, but it has movement-heavy combat that feels more or less seamless. If you run up behind a monster that is currently moving, you'll hit it when it feels like you should it it. In FFXIV, if you're a melee character trying to hit a moving monster, good luck. That's an example of trusting server-state versus client-state in virtually all cases.
I'd go further and argue that SE shouldn't have taken this approach. When people compare FFXIV's responsiveness to games like WoW, or GW2, or TERA, this is what they're talking about. And it doesn't just affect combat - even things like Gathering are prone to it. Ever notice the slight delay between when you try to harvest a point, and when your character actually begins the action? That's the wait time for your client machine to send a packet to the game servers, receives confirmation of the action, and then is told by the server to engage the animation. That's bad design. The action should begin immediately, controlled entirely by the client, with a packet being sent once to the server indicating what you did. The server should briefly check how reasonable the action is based on your character's state (to avoid hackers gathering on, say, a White Mage), and then it should send back the result of your action. If you have high latency in a scenario like this, it might take a couple of seconds to see your reward from a given swing - but in the meantime, you can initiate another swing or two, and not waste your time sitting at the mining point. The server backlog will catch up when it catches up.
That would be my preference anyway. It's closer in line with what other major MMOs do, and the responsiveness difference greatly improves the feel of the game. Nobody likes wrestling with a user interface.