I think the execution of the token system isn't a good thing in the first place. Seems like tokens should be used to soften the blow of not getting a drop, not be the single most important thing for all loot.
I don't like how that makes players feel/act (they can make easy time/token comparisons), how it basically allows the game to be a matter of grinding duty finder parties (as an asshole, if you wish) instead of joining a static group for the most of it, and I don't like what it does to crafters and gathers (I don't understand why this game doesn't employ more Monster Hunter-ish crafting for pretty much all endgame gear, with crafters synthesizing stuff from rare/ex items from other player inventories (plus harder to obtain gathered materials which work in a sub-system that isn't so brainlessly easy to bot or crash the market of, i.e. a new gatherer endgame to match this new crafter endgame). To me, something like tokens should be used so no players feel they got nothing from the run and casual players can get loot over long periods of time without ever joining a group. As the main form of progression, it is way too manipulative and obvious for my tastes.
The proper solution to the AK speed run problem was to make a portion of tomestones consistently and predictably drop from enemies. The solution to AK being a bottleneck would be to improve the rewards of other dungeons (in fact, I'd say they need to think in terms of content not being outdated so quickly, doing 3 dungeons over and over is better than doing each one over and over consecutively. Dynamis was a grind I didn't like, but at least you had five "dungeons" to do, in addition to a bunch of other content), give minute amounts to those who redo story primal and lower level dungeons (more so to make helping new players not seem like a complete waste of time to those who are little obsessive about it), and add it to other types of the content. The latter, I admit, isn't a very suitable fix given how stupid and easy to break stuff like FATEs are (which makes up most of the content in the game putting aside the main scenario). Maybe a more controlled type of FATE is in order for end-game content, one that is activated and limits participation. I was thinking if need/want/pass loot system even comes down to deciding the fate of major loot, then players should get rewarded tomestones whenever someone else in their party gets a piece of loot (maybe a bonus for passing an item they could need).
As for rushing people through cutscenes, a fun solution would be getting bonus tombstones for helping new players - but only if the new players allowed that player to get it. So, you would award players who were patient and kind and players who weren't wouldn't get this bonus. I also feel like a small nerf to some of the tactics used in Castrum Meridianum may be in order, mainly the part where people use those launchers to kill enemies instantly.
In FFXI, EXP at 75 could be used for merits. In this game merits would probably just mean more points to allot. Not much room for customizing classes through lowered recasts, new actions, etc. since they seem to want to avoid that kind of stuff looking at the design (if everyone plays the same it is easier to balance and is... "less stressful").