Yeah the Mass Effect series plot falls apart starting in 2 and really collapsing into stupidity in 3, 2 is often overlooked because the companions are all good characters and have interesting stories and most of 3's numerous problems are overlooked because the ending is so awful it distracts from it. In the end ME2's plot outside of turning Cerberus into the villain sue organization and the Arrival DLC has no real significance in the series plot as a whole. Smudboy on youtube has a great analysis of the problems of its plot and Spoiler Warning covered it more thoroughly in a Lets Play. Basically all the problems you're seeing never get answered, plenty of other people have noticed them as well, and really they only get worse.
As sad as it is its probably best (imo) to consider the reaper threat ended after 1 and consider 2 and 3 noncanon fanfic expansions. 2 Does give some fantastic characters but thats about it, and 3 has only one good sequence from Palaven through Tuchanka which is mostly only good for the interplay between the characters of Wrex and Mordin.
As sad as it is its probably best (imo) to consider the reaper threat ended after 1 and consider 2 and 3 noncanon fanfic expansions. 2 Does give some fantastic characters but thats about it, and 3 has only one good sequence from Palaven through Tuchanka which is mostly only good for the interplay between the characters of Wrex and Mordin.