Why Geth and Quarians won't be in Andromeda and why you should be ok with it.

With the arks departing before the Geth made peaceful contact with organics, how would you justify their involvement? Legion gave way too much highly specific information to suggest that other platforms were off building bridges as it was.

Additionally, people clearly thought Shepard was borderline insane for trusting the Geth in every circumstance in which it came up (which were admittedly few, outside the quarians and crew.) The galaxy does not trust the geth. Their only experience with them is the Morning War and the Geth War of 2183. In 2185, there is no grounds for a relationship.

You're okay with retconning this, when you've complained about even the hint of any other breaks from lore?

I think there are low chances of every species be in Andromeda though. They avoided one of the major problems in leaving someone behind by making the project separate from the Reapers' threat.
I do hope we'Il get more then the confirmed 5.

Batarians ought to hijack the Hyperion -- maybe that's why it's lost!

I tell you, these stories just write themselves.

Hey, if Bioware is retconning everything anyway they may as well retcon something that goes my way for a change.

In all seriousness, there are ways they can explain that without retconning. For example even if the AI is not a secret, Geth involvement could be since as you said they weren't seen as friends at the time. So some deal could have been made where the Geth help and those Geth can come along, and in exchange their involvement is kept secret to avoid both political blowback for the project and reprisals on the helpful Geth, especially in the last couple years. Thus when Legion is talking to Shepard, he keeps his fellows existence secret. After all Legion may trust Shepard a lot, but he doesn't tell us everything. Plus he may not consider them Geth just like he doesn't the Heretics, so he is technically being honest still. 

The Quarians weren't monolithic. Not all of them wanted to retake their homeworld. Out of, what, 17 million Quarians you don't think any of them would be interested in traveling to another galaxy?

It makes little sense to have Krogan when they can't even own battle ships and their central government is pretty much in ruins (only getting a bit better with Wrex in command) but not other species like the Quarians or the Volus (the galactic bankers).

Based upon the info we've been given, this isn't a "set up a new civilization" effort. They are going to establish a foothold in a resource-rich sector of Andromeda. They are supposed to setup the means for future travel to and from the Milky Way. The Volus will (in numbers) come later, when the credits start flowing.

Regardless, the Krogan are the best warriors in the galaxy. Hiring or recruiting a large number of Krogan when going into unknown, potentially hostile environments is good thinking. They are both more fierce and more robust than any other crew you could field. 

Even if the asari are more skilled, the krogans are more resistant to harsh environments, as well as being more durable, with their regeneration and multiple organs.

If everyone in this game is smart and wears the proper attire, harsh enviornments shouldn't be an issue. Plus again, mechs would be able to handle harsh environments and be more durable than even krogan. 

To be fair, the Genophage isn't something that needs to be solved. Since whatever world they find will probably be less hostile than Tuchanka, their population will slowly grow. After all with the Genophage they have the same average birthrate as humans do. 
But other than that, I agree with you.