Most likely this was stated in several other threads and will be in future ones.
The Queue system ensures you can play with the build you want without having to suffer exclusion from game content. If there would be no benefit in queueing over premade parties, then something would happen a friend once described for a different game:
The utter **** of builds/classes would be taken care of by group consensus or natural selection. Same principle for toxic player behaviour.
Only thing I am really concerned about is that the system bypasses your own blocklist. I can tell cause i ended up having to do 3 145 runs with a blocked toxic player.
As for missions, queue can be hit or miss. Ever done a run as the heal with everyone else being 15 lvls below you ? The horror.
The fact that queue also produces healerless parties was a major factor that made me play cleric as main character.
Some specific issues have also been stated countless times, but some from me:
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Monster Support, in various forms such as:
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Outbuffing a +154 Bless with +24 (the priest that did that didnt even respond and went on doing it, ~170 mission)
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Pulling bosses out of Elementalist AOEs
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Icewalls that end up protecting the mobs cause they prevent melee from reaching them or eat up bullets
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Some higher rank cleric class players that had been cleric2, priest or krivis refuse to buff cause they are [insert high rank class] now, most notably paladins do that.
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Classes that have high dmg/high cd skills throwing them at the furniture stack or trashmobs near the torch
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People queueing, then rushing the boss down.
For two cleric issues, I have to defend the “offenders”. The often bad heal placement results from how heals work in the game. As with every other skill that has multiple charges, these do not have independent CDs. Therefoe to maximize heal output, the skill must be kept on CD. Often it is just enough to turn around, throw down heals, then face the boss again. Casting heals only when actually needed is something for mass heal of priest, not the generic cleric heal.
A low safety zone usage most likely results from their tendency to attract EVERYONE like meat attracts piranhas. It is certainly not good for 5 players to sit on one tile that is only safe for a limited time.
Sure, some coordination talks are nice, but since most content is fairly repetitive, people get tired of explaining. Best example of this is the question whether to do poata and mole at the same time or not.
EDIT: Oh just remembered a very notable issue both in rush and queue.
It is the lack of waiting time for others or CDs. In one 130 fullrun, before boss1, I would have needed 15sec for heal to become ready. But cause someone went directly at the boss without all buffs on, it eventually led to the healing not being enough and some deaths.
Or once I suffered a bad lag in loading screen, also being the only cleric class in the queue party. The four others rushed at the mobs and by the time i reached them, three had died and started flaming me.
This also applies to shouts for runs in global. People start the run once the party is full, not really caring that cause of the global shout, others need to get the dungeon first.
or tighter instead of a doughnut 
)