This is just going to be a short list from me but if you want to add feel free. (provided your complaints are aimed at low tier missions, or items, etc.)
Punch/Pummel gun vs Magnus: These used to be basically the exact same weapons (mechanic-wise), after the GU both no longer knock you prone but the Magnus charge bullets now plow through enemies while the Punch and Pummel guns are left the same. Why do this? This gives new players the wrong impression of this type of gun. When they get to the HOH and see the Magnus (which obviously looks similar to Punch/Pummel guns) they will remember that trash gun handed to them and not spend their CR on it (or their CE for that matter).
_____________________
Lack of bomb diversity: all T1 bombs are basically blast bombs. In this game we have so many types of bombs yet new players are only given one. New players are also not given any bomb boosting gear in T1 (but they are given Gun and Sword boosting gear). Plus they aren't even made to use the bomb in the tutorial, basically Rhendon hands you a bomb, explains the mechanics, and then sends you off to Haven with no actual experience in fighting monsters with that bomb.
______________________
Non enforced tutorials: Basically players skip through the tutorials and then plague the rest of the knights in the game with questions that the tutorials answered. The Speech prior to the Vanaduke battle and the Arkus battle is enforced. Tutorials are just as important as the story if not a bit more.
I didn't know about the punch/pummel gun problem
That really needs to be fixed, heavy guns are way more useful than before
About tutorials, that really needs to be mandatory, I've seen defender elites who don't know how enemies are affected by damage types, some didn't even know if it was Kora or Hahn who tell you about missions