Well by all accounts, they left sometime around either Arrival happening, or when Shep was in the Brig, after which all heck broke loose, so please pardon Shepard not pontificating about a crack-pot organization that "left" and then went stone cold dark and no one will know what happens to them back in the Milky Way, probably ever, or for 6 centuries. Also consider, Shepard was dead for 2 years, then working for Cerberus out on the fringe, not much on core worlds, and was busy with Collectors, probably didn't care what some socialite wannabe explorer was doing. Shep was kinda busy with other things all during the time this was going on, so meh, so me personally, easy explanation and nothing to worry about.
Please consider how many "disgraced" members were apart of the teams, and know that many publicity/news outlets may not have hyped it all that much when they left, other than say good riddance, because they were disgraced and black ops operatives. As for AI's, they were produced by more than one company, it just usually winds up causing trouble for whoever does it, either with the Citadel or going rogue....paging EDI to the Citadel Security office.......Cerberus cleanup on planet Aite, cleanup on planet Aite....
Honestly, I have no idea how they are going to deal with Andromeda, personally, I wish they would just continue that story line and let Milky Way/Shepard be done. Not going to happen, but that is what I wish they would do.
Just because you/Shepard didn't hear about or care about the Initiative doesn't mean there are separate time lines, just means Shep didn't care or think they were alive....please consider no one in the MW knows what happened to them, and the Arks were radio silent.....MW probably thinks the Reapers killed them or the Arks are wandering space as Ghost ships.
