These are the things I learned from that experience.
Like the main website says, feeding fruit to a Chao reduces its hunger and increases its tiredness - the only reason a Chao will not attempt to finish a fruit is if it is disturbed in the process. Feeding a newborn Chao about two dozen pieces of fruit will boost its magnitude to the point where it evolves.
I have reason to believe that coconuts MIGHT increase the stats of a Chao. My Normal-type Chao has never been given any animals and has never met a character or been fed in Chao Adventure, but Chao Adventure and Chao Editor both show that several of its stats are in the double digits.
The biggest difference involving food is that it appears to be contact-based. If a Chao and fruit collide, and if at least one is in motion, the Chao will attempt to eat the fruit. As a result, Big and Gamma struggle to feed Chao unless the Chao is at a higher elevation or if the characters are in the middle of placing or picking up the fruit. Even if a Chao is asleep, it will attempt to wake up and eat a fruit it comes in contact with. These things also apply to animals. Luckily, waking them up like this doesn't seem to upset them.
You might want to move any fruit you take out of a VMU if you plan on taking multiple Chao out since they land in the same place. I accidentally had a Chao go into a Lifenut-based mating season because of this.
As mentioned above, my Normal-type Chao's stats indicate that coconuts appear to give slight stat boosts as well, and judging from my main Chao's other stats, there seems to be a chance that the stat boosts given by animals as listed on the main website appear to be wrong, and instead more close to what they are in SA2DC. One of my Chao has mainly been given rabbits for all of its life, and its Fly and Run are relatively high while its Power is abysmal.
Giving a Chao an animal or feeding it will turn their emotiball into an exclamation mark. It only seems to turn into a heart when a Chao is jumping up and down to express high happiness. Food and animals boost happiness (except for the Lazynut) and apparently picking them up does as well.
I've heard rumours that the increase in stat power in races is NOT linear. Apparently, a Chao with 999 in a stat is about twice as proficient as if it had 998 in that stat.
Station Square aside, I'd take the SADX ones over the SA1DC ones any day of the week. Giving Chao who are in the Mystic Ruins and Egg Carrier gardens animals is a nightmare.
Chao in the Mystic Ruins garden tend to spawn in the geometry of the garden, making them inaccessible and invisible. If you're planning on giving a Chao in this garden animals, either put them into Station Square or the VMU prior to collecting animals just in case. The camera is very prone to getting caught on the garden decorations, and it is even easier to kill yourself than it is in SADX.
The Egg Carrier garden's spawn point, water depth and player boundaries mean that almost all of your animals will immediately go under the teleporter platform and swim out into the ocean. It's not worth getting more than one or two at a time. The whole garden feels cramped because of the central area's hills unlike the flat terrain in SADX.
Also, Flying-type animals tend to fly around in SA1DC. Makes them a hassle to grab most of the time and the hardest to retrieve in the Egg Carrier garden.
There appear to be ten colours in total - normal, gold, silver, black, gold + black, silver + black, amethyst, ruby, sapphire and emerald. I believe that amethyst is the colour that can be obtained from breeding a gold Chao and silver Chao together in Chao Adventure - Sonic Retro says that the only ones available from SA1DC's black market were ruby, sapphire and emerald. Yeah, apparently the SA1DC site had a black market.
In the files, there appear to be two variants each for the silver and gold textures (maybe one of them is used to colour the eggs - if you look closely in the garden you can see that they're not completely opaque), and the other four jewel textures have this weird opacity gradient going on. There's also a burgundy jewel texture there as well. Don't know why, but it's there. Looks like a mix of the DC and GC ruby textures.
One thing that stands out the most is the emotiballs of Chao who are at least partially black. The tinting system used to give them their colours also affects their emotiballs and makes them pretty dark. You might be able to see this on the main website if you check out Chacron's section. The tint messes with his emotiball as well, and since he's darker than other black Chao the emotiball also has more blackening as a result.
Black Chao's emotiballs look like they're yellow when they're still children without stat influence. Maybe the game gives normal colour young Chao and Normal-type Chao a slight blue tint to turn their yellow parts into green, emotiball included.
The Chao that result from breeding a black Chao with a gold or silver one on a VMU use the textures of the jewel Chao with the black Chao's complete body tint effect - they don't use their own specific files. As a result, the jewel specular is tinted black as well.
This INCLUDES Chaos Chao. Be warned.
Throwing a Chao does not appear to make it lose HP, regardless of what it gets thrown into. Outside of fights in Chao Adventure, the injury system seems to work on a basis of negative actions hurting a Chao and/or making it unhappy. On the subject of Chao Adventure, you might want to restore a Chao's HP before taking it out of the VMU, especially if it has lost a battle. There are rumours that taking a 0 HP Chao out of a VMU or even losing a fight will cause it to die shortly after returning to the garden.
Any action that can injure enemies can injure Chao. Jumping next to a Chao with a character whose jump classifies as an attack will hurt them, and Gamma is capable of using his laser to lock onto Chao.
A Chao that is close to dying, either through low HP or old age, will be slouching as it walks around. When a Chao goes into the death cocoon, the emotiball will not change and there will not be a death fanfare.
Like I mentioned before feeding a baby Chao about two dozen or so fruits will get it to cocoon, and the VMU-exclusive fruits that boost a single stat do not appear to affect the sliders. The cocoons for both evolution and death are very pale blue and have a shape that resembles a Chao Fruit rather than being completely symmetrical on the horizontal axes.
The biggest change here is that a Chao's sliders, at least the ones used for the first evolution, DO NOT reset after reincarnation. When I was creating some Chaos Chao, the second Chao I was using ended up trying to become a Power-type despite having not had any animals since it first evolved. A couple of Run group animals rectified that and got it to go Normal-type, though. This is what I get for giving them koalas to ensure they'd be happy enough to reincarnate after having very short lives.
Additionally, Chao who have reincarnated appear to evolve much quicker than Chao on their first life, and usually take less than a dozen fruits to evolve.
I have a couple of other Chao who I can test this out with since they've gone through second evolution. I however can't do it with Marine, my eldest one, as he's a Run/Run. The others happen to have different secondary types though, so I'll try to see what types they attempt to become without any animal influence once they reincarnate.
On the subject of Marine, the second evolutions in this game are insane, ESPECIALLY for the Fly and Run-types. Marine's run/power slider has gone to the run side so much that his ears have grown to being nearly as big as his head and pretty much broken his model. The Fly-types' horns grow immensely during second evolution as well. I wonder if they're similar to what happens to Chao if you remove the adult magnitude limit in the future versions, minus the whole opacity issue thing?
I've been meaning to experiment with how many animals it takes to align a slider to the point it sets the current evolutionary path, but I haven't gotten around to it yet.
A Chao in mating season will have flowers bloom around it like in the other games, but these flowers pop up in random spots rather than in a circle and make noises when they do so. The emotiball remains the same as well. They also don't have a specific breeding animation as well. A Chao that is planning to breed will get a question mark or look up/down with every slow step it takes towards a Chao in season, until eventually the egg(s) pop up.
The biggest thing here is that it's not guaranteed that both Chao will successfully breed. One Chao might produce an egg and go out of season while the other doesn't, both might do it relatively simultaneously, or one might do it after the other (even if the first is currently in a cocoon reincarnating). I wouldn't be surprised if this happened because of a glitch.
Yeah, it's a mess.
Successful mating done via Lifenuts will cause a Chao's lifespan to decrease rapidly - from what I've seen on Chao Editor I think it might knock them up a couple of life stages? I don't know, I'm just guessing from when I accidentally let one of my Chao eat a Lifenut. I didn't test either of my Chaos Chao for some reason. Regardless, a freshly-evolved adult Chao will immediately die after three Lifenut-based breedings. The Chao I wanted to go Chaos actually did so later than the other one because of the whole issue in the above paragraph, amongst other issues related to evolution.
I've also yet to test out cross-colour breeding in the gardens. Since I don't have access to a physical VMU as I'm using emulators (ElysianVMU supports multi-instance communication at least over the internet but doesn't currently support true saving), I can't do any VMU-based tests. What I am able to do though is hack in some special colour Chao using Chao Editor and then breed them in the gardens. I'm probably going to draw up a table at some point to use as a reference.
As mentioned above under injury, Chaos Chao can and WILL die if they lose all of their HP. I'm pretty sure they can't die from aging as usual, though, and they do need to be happy enough and set to become a Normal-type in order to successfully evolve after being given all 15 animals. Keep that in mind when a Chao with stat sliders out of the neutral ranges reincarnates because of the whole retention thing.
The thing that is the most noticeable about Chaos Chao is their complete inability to express emotion visually. They can't close their eyes (not even when sleeping) and their emotiball will not change at all.