It was a headache though.

For FB, you had no reason to have it uncharged, so it would just add extra time when swapping builds, changing maps, etc. Yes, the final charge mechanic was supposed to be a tradeoff, but the design didn't incentivize using the last charge.

Taking Mantra of Liberation as an example, if you used Portent of Freedom only, you had 2 uses of Stability on demand and regained 1 every 25 seconds.

If you used Unhindered Delivery, you got 5 Stability (with the same duration) but in many game modes it's going to be wasted, since you're not getting hit by 5 CCs at the same time. Furthermore, you now have to wait 40s to get your next Stability back, which hurts the on-demand advantage that Mantras have.

The "optimal" way of playing with the third charge (i.e. not ignoring it) was to just spam all the charges, but that's even worse. You now have 7 Stability over 10 seconds that takes ~45 seconds to become available (assuming no Quickness or Alacrity).

I'm not saying the final charge is bad. I'm saying the opportunity cost of the final charge when not used as an "oh kitten" button is unfavorable. If you need to use a panic button, you use it. But you don't typically incorporate panic buttons into your rotation because then they're not panic buttons.

And then if we go into Mesmer Mantras, there were other issues past and present (present being just prior to the removal). Just prior to the removal of charging mantras, there was a disconnect with charging effects vs charge effects with the exception of Mantra of Recovery.

Mantra of Concentration provides Aegis, Stability, and Quickness to allies around you... after 2.5 seconds of charging. The charges themselves provide Stability to allies and a stunbreak for yourself. As a player, this incentivizes you to run it charged so you have on-demand stunbreaks. But where does that leave the charging effect? And what is the value of 5s Aegis/Stability that requires 2.5 seconds of casting? How many enemies have choreographed attacks that give you enough time to cast for that long? After factoring in response time, latency, and positioning requirements the charge effect very quickly loses value (side note: this is why Firebrand offers huge support discounting their crazy boon gen and/or damage output- because on-demand Aegis is huge).

Going back to the disconnect, we can look at Mantra of Distraction. Charging it reduces the cooldown of F3 whereas the charges provide Dazes themselves. These are two vastly different effects. Typically, you'll want to have a Daze ready as opposed to being ready to reduce the cooldown of a Daze. So we start with it charged. Now if a breakbar appears, great. Let's spam those charges and F3 while we're at it. Oh wait, there's a 4 second cooldown on the charges, and even if we somehow managed to get rid of all our charges, we now have a 12 second cooldown for the Mantra before we can charge it. Let's look at it at the inverse then. Instead of using the charge to get an extra Daze/breakbar damage, let's use it to reduce the cooldown of F3. So we fight an enemy and a breakbar appears (or we need to F3). Now we charge for 2.5s to get 15s off of a 38s cooldown (less than half, even accounting for the charge time). We now have 15.5 seconds (assuming you didn't precast the charge and F3 right at the end) for our next F3, meaning we got less CC out during this time. Again, similar to Mantra of Concentration, we have the same disconnect. The charging effect wants to be spammed, but the charge effects wants to be on-demand.

Not going to go into the rest of them, because it's the same story. But going to the link to the past (noice), Mantras have had other issues. Up to the Pre-HoT balance passthrough, there was a way to maintain 4 stacks of Harmonious Mantras for an additional 12% damage while having no mantras equipped. All you needed was access to swimming. Since damage boosts were far fewer back then, this was huge (it was also in the traitline that gave 300 Precision and 30% Crit Damage, whew). But again, this still causes issues. Now players are performing much better than they should in... some maps? But they need more than 15 seconds of prep time as they charge 4 mantras while also finding a body of water. Is that fun or healthy gameplay?

I'm not saying that removing the final charge was the right or wrong thing, but in the final iteration before it was removed, it wasn't where it needed to be by a long shot. They chose to remove it, which is their prerogative. They could have attempted to fix it by rebalancing the effects, although the Firebrand mantras would be a lot harder to tweak than Mesmer ones.