I think a major issue is how the tower works. I understand that It's a nice little spot a bunch of devs took time and effort to craft but at some point I don't want to have to load it up everytime I want to decript something. Allow me to decript at least from the menu where my ship is flying, no need to go all the way to the tower. pretend the ghost can direct link to the criptarch or something.
Also, why the hell does the weapon vendor even exist? If you bought anything from him during your whole playthrough let me know because I'm probably missing something here.
The guy who posted here earlier is right, no green loot should ever drop once you've reached level 21+. Allow me to buy crafting materials and there is no need to collect dumb, useless, green loot.
Lastly, allow matchmaking for story missions. I can deal with the mission variety being complete garbage, but it would be a lot less painful if I had some random people to share the boredom with.
There are bigger "core" issues but these ones irk me right now, especially since I can't seem to stop playing the game despite all its flaws.