I pulled a TL:DR especially because some of those signal a lack of attention on your part or simply lack of curiosity by not reading the codex, so to correct some that I did read:
- Saren is a Spectre, the right hand of the council. In my country we have an expression that translates best to "drying ice", which in this case means the Council/C-Sec only sent Garrus to investigate as a mean of placating the public.
- Technology advances, evolves. So Thermal Clips are not the wildest invention. ME2 (and 3) also saw the invention of countermeasures to omni-gel as means to break into doors and locked containers.
- Joker is not and never was a cripple.
(Perhaps the most blatant ones in the "lack of attention" department)
- Of course the Reaper ship (Derelict Reaper) has Cerberus insignias and a decontamination chamber. There was ACTIVE INVESTIGATION going on by Cerberus before Shepard arrived to find the entire survey team dead/turned into husks and abominations. Why would Cerberus not create it's own improvised instalations?
- Kasumi was not let in because HOCK KNEW WHO SHE WAS, and he says so at the vault later.
- Sovereign was defeated by a "bunch of ships" (it was an entire Alliance fleet, but I suppose you do not pay attention to details either) because it essentially shifted it's attention from it's own body to Saren. So when Ultron Saren is killed by Shepard, Sovereign has it's own barriers and countermeasures destabilized and shut down, and EVEN THEN it took the full power of Hackett's entire fleet to bring it down.
I usually do not judge people for their attention span, but yours is concerning.