Uhh.. Jonah wrote...
It deepened the universe, and we also learned the truth about what exactly happened to the Protheans.
What did we learn?
We now have three stories:
ME1 - the Protheans lost the Citadel and the relays in a surprise attack, what remained of the Empire after this intial blow got harvested over the next decades or centuries safe for a few hidden pockets of resistance like the Ilos facility
ME2 - the Reapers tried to ... um, ascend the Protheans by turning them into goo for a new Reaper, when this failed they kept a few indoctrinated clones around for ****s and giggles
ME3 - Javik's stories don't mesh too well with what we learned in ME1 and ... has little to do with what we learned in 2
Someone said that from ME2 on the writer threw themes and ideas at a wall to see what stuck. The Protheans are a good example.
ME2 deepened the universe mostly by introducing conflicting or irrelevant information and elevated retconning stuff - accidentally or on purpose - to an art form.
It also headed down the path of making factions as flat and one-dimensional as possible (Alliance = morons, Council = morons, asari = arrogant, geth = misunderstood underdogs, quarians = morons, krogans = victims).