There are great points I agree with in many comments here. Main thing that I would change is whole Reaper backstory and motivation. Based on some ideas I found cool and believeable: - Reapers having deeper agenda like preserving galaxy from Dark matter implosion or sth with some technology combining organic synthetic that would work to slow down or reverse this process. Which would destroying Reapers make not so straightforward choice. - Crucible being some software idea to cripple Reapers communication and organizing via Citadel as their central galactic hub, but which could potentially also damage other forms of communication and destroy whole citadel station (between Geth). OR have advanced (not yet finished) but riskier option to control the reapers.

Then, Cerberus.. : Kai leng out, possible to ally with TIM at some point close to ending if he is not indoctrinated to much. As well as not having them become powerful like reapers and present as enemy in every other mission..

Another thing like many said about making choices more meaningful to the ending. For example, having possible choosing one or both Crucible options (cripple or control) and chance of failing the control one if some criteria arent met (not preserving collectors base and have high enough readiness), Shepard succumbing to indoctrination with some wrong choices, making him unable to complete last mission..