I was just rewatching
this (great review by sfdebris btw) as I noticed something: he talks about how in ME2 your main enemy are the Collectors and that there is lots of talk about it, but you rarely face them, only in 3 missions to be exact.
Now in ME3 the focal point is again the Reapers, and there are again 3 missions that actually are about defeating them, but again you never really take out one of the big ones.
And another thing he mentioned at the end of the review: "but the frequent references in the game is to humanities wide genetic variance, not to mention the plague on Omega was to force such mutations on other species" note that these references aren't only by Harbinger, but also as a side note in Mordin's loyalty mission. Now if we look specifically at synthesis: does this in any way support any genetic variance? I guess not, as one of the goals is to make something more equal.
I don't think BioWare would just drop this. Also Tali specifically mentions Haestrom in ME3 while mourning after Legion sacrificed itself, Freedom's Progress is never mentioned, it's mentioned in a dialog when doing the Tuchanka bomb with her (seems again like ME2 is was planned to be more open instead of streamlined), and it's a side note for a conversation with Liara when choosing her for the Dreadnought.