Okay, good news everyone! It turns out there are 3 secret Chao Eggs hidden in Sonic Adventure that if we go for them first thing, we can probably snag. Here is a link discussing how to get all three
Secret Chao Eggs. Plus, as long as we don't choose the Other Egg Carrier, we should have immediate access to one of two of the eggs.
If we choose the Egg Carrier, we just need to make a quick jog down to the prison inside the ship and press some buttons to open up the cell the Black Chao Egg is locked in. Normally only Amy or Gamma would be able to access this area, but if we trust our new Metal Sonic to not break things, we could send him to do it quickly.
In fact, the Metal Sonic is probably our best bet in sending to retrieve the eggs due to his speed. We want to be in and out fast of some areas.
The Egg Carrier Chao Egg is probably the least risky to get due to it being on our own turf, unlike the Golden Chao Egg in Station Square and the Silver Chao Egg in Mystic Ruins.
I've already described how the Golden Chao Egg is in an Antique shop and you essentially have to pull an Indiana Jones and switch it out with a rock so you can get out with it, but one thing we need to keep in mind is how we get to the shop and back to our base without the main characters noticing or running into us. We could check the timelines of the various plots and try and coordinate getting the Golden Chao Egg with whenever the most people are out of the city.
Now, I know if we choose the Ancient Ruins we will be close to the Silver Chao Egg, but there are some complications in getting it. Said complications is that is is hidden behind a waterfall in the lake which directly across from Tails' Workshop/House. When we go for this egg, we will want to probably stake out Tails' Workshop first and wait for him to leave before we go for the Silver egg. Once again, we need to worry about getting to and back from the area with the Egg without being spotted.
Ultimately, I think focusing on us acquiring the three eggs during Adventure will be the best course of action. I believe this because Robotnik and what we have him will be doing the majority of the fighting, and our job is to research.
If we need permission to send out units to get the eggs, we just need to pitch the idea of researching Chao to Eggman. Which I think we can do if we emphasize the Reincarnation aspect of the Chao and how we could research that. He seems like the type to find immortality appealing. Another aspect we could try and pitch is rapid evolution, but that may not interest him due to focusing on robotics. He might be interested in the innate levitation of the Chao's head sphere. If we could utilize that, we could make self floating troops, no jet packs necessary. The ability of the Chao to shape said spheres to match their emotions implies it being a liquid of sorts or perhaps illusionary. Either way, both would be good research material, as the former could allow us to make robots that are semi-liquid, as in they are mostly fluid but have an solid AI core with whatever is necessary to manipulate the fluid, or we could make liquid controlling robots. Which actually might be the best pitch the Eggman if Reincarnation doesn't work, as Sonic's biggest weakness is water. With these Robotic Waterbenders, we bring the water to Sonic, making it so he can't just avoid it. These things would probably become Sonic's worst nightmare. Illusions would be cool too, but the ability to manipulate liquid is more threatening to Sonic.
Anyway, I think this concludes my pitch to why we should get all the Chao Eggs. I once again want to stress the necessity of getting all three eggs. Eggs hidden in the world map are only a thing in Sonic Adventure 1. In 2, you have to buy them, but that requires access to the garden in the first place. Eggman does get access there, and we could ask him to bring an egg or two back, but it would take far longer to get more Chao due to having to buy eggs. Plus, the Garden is shared between all player characters, and I think creating our own personal Chao Gardens would be better so we can control what animals they are given and how they absorb Chaos Drives in Adventure 2 to raise their stats.
The only real difficultly I can see with us raising Chao is that if we don't have alignment fruit, due to us falling on the villain side, we will likely mostly create Dark Chao when Chao evolve. Which is a shame, as there is three specific and very hard to get Chao evolutions I want us to try and get after we figure out how the Reincarnation works.
Said evolutions are the
Chaos Evolutions. Specifically, the neutral alignment Light Chaos, he dark alignment Dark Chaos, and the hero alignment Hero Chaos. These Chao are extremely hard to evolve into, but they are immortal. This opens up the avenue of researching immortality. We can't evolve any Chao into them right off the bat though, as the Chao has to have reincarnated at least twice before they can possibly evolve into a Chaos Evolution.
I think that covers my continued pitch for Chao. Here is the page on
Chao on the Sonic Wiki.