The one question I am still left with is: How do the fauna compare to each other?
The short version is:
1) Amoebas should be considered the default fauna and they're best when using SC centered designs. Their downside is they can only grow to large size, but on the upside they skip the medium size stage.
2) Crystals are just bad because they are fragile and while the early growth stages make up for it with speed, they lose all their speed advantage as they grow, but stay squishy.
3) Cuthuloids have good offense, great armor, but low hull and low speed in their final stage. They grow from medium through large to huge size.
4) Tiyanki are tanky, but slow. They are the only fauna with four growth stages, from small to huge.
5) Voidworms would've been perhaps the best fauna, except there seems to be a bug with the adult stage (or maybe it's deliberate) where either it uses too much naval cap (they're size 8 instead of size 4) or their component size is too small (they use L components instead of X). Either way their mutations are half as strong as they should be given how much naval cap they use up.
5) Voidworms have a thing where adults use 8 naval capacity, but only use size L mutations. However, groups of 3 adults will eventually combine into size 16 troikas, which do use X sized mutations. They still have a disparity between mutation size and naval cap usage though, which makes them less generally useful. Troikas do have 3x the hull and armor of adults and twice as many innate weapons and they have 3x Regenerative Hull Tissue, so they have good base stats, they just are not at all efficient at utilizing mutations.
Effectively this leaves us with three types of fauna worth using: amoebas, cuthuloids and tiyanki. Amoebas are the fastest. Cuthuloids have the best offense and strong armor, but are slow and have low hull. Tiyanki are the toughest, but slow and have the weakest innate weapons.
Now for the long version with the base stats of all growth stages:
AMOEBAS
Amoeba Weapons are an energy weapon that deals +25% damage vs armor and +33% vs hull. Amoeba Flagella are bombers with 100% shield penetration and +50% damage vs armor. They have medium hull and armor and don't lose speed as they grow. Fully grown amoebas will be slightly slower than battleships. They are the natural choice for a design centered around strike craft.
Space Amoeba
Cost: 500 Food
Size: 1 (Corvette)
Mutations Size: S
Natural components: 3x Small Amoeba Weapon, 1x Regenerative Hull Tissue
Hull: 300
Armor: 100
Evasion: 65
Speed: 100
Space Amoeba Mother
Cost: 1900 Food
Size: 4 (Cruiser)
Mutations Size: L
Natural components: 1x Large Amoeba Weapon, 2x Small Amoeba Weapon, 1x Amoeba Flagella, 1x Regenerative Hull Tissue
Hull: 2000
Armor: 1500
Evasion: 30
Speed: 100
CRYSTALINE ENTITIES
Shard Throwers are a kinetic weapon with +50% damage vs hull. Crystals start out much faster than other fauna, matching corvettes in speed. But as they grow they become slower until they are a little slower than battleships. They have weak defenses too with no natural armor and bad hull progression. Shardlings can be nice for their speed, but don't let them grow. Amoebas are better in almost every way, except initial speed.
Saphire Crystal Shardling
Cost: 300 Minerals, 15 Rare Crystals
Size: 1 (Corvette)
Mutations Size: S
Natural components: 3x Small Shard Thrower, 2x Small Crystal-Forged Plating, 1x Regenerative Hull Tissue
Hull: 520 (300 base, 220 plating)
Armor: 0
Evasion: 60
Speed: 160
Saphire Crystal Shard
Cost: 500 Minerals, 25 Rare Crystals
Size: 2 (Destroyer)
Mutations Size: M
Natural components: 1x Medium Shard Thrower, 4x Small Shard Thrower, 2x Small Crystal-Forged Plating, 1x Regenerative Hull Tissue
Hull: 870 (650 base, 220 plating)
Armor: 0
Evasion: 35
Speed: 140
Saphire Crystal Quintessence
Cost: 700 Minerals, 35 Rare Crystals
Size: 4 (Cruiser)
Mutations Size: L
Natural components: 1x Large Shard Thrower, 4x Medium Shard Thrower, 2x Small Crystal-Forged Plating, 1x Regenerative Hull Tissue
Hull: 1620 (1400 base, 220 plating)
Armor: 0
Evasion: 15
Speed: 100
CUTHOLOIDS
Meteoroid Slingers are kinetic weapons with +100% damage vs shields, -50% vs armor and 120 range. Devouring Maws allow Cutholoids to eat ships that are 1 size smaller than them, so the biggest ones can eat cruisers. They have low hull, but great armor. They start out fairly speedy, but get slower as they grow, so that a Cutholoid Hatchling is faster than a Space Amoeba, but an adult Cutholoid is slower than an Amoeba Mother. They make good "tanks", but watch out for armor penetration.
Cutholoid Hatchling
Cost: 1200 Minerals
Size: 2 (Destroyer)
Mutations Size: M
Natural components: 2x Medium Meteroid Slinger, 1x Medium Devouring Maw, 1x Regenerative Hull Tissue
Hull: 200
Armor: 1000
Evasion: 15
Speed: 120
Cutholoid Juvenile
Cost: 2100 Minerals
Size: 4 (Cruiser)
Mutations Size: L
Natural components: 2x Large Meteroid Slinger, 1x Large Devouring Maw, 1x Regenerative Hull Tissue
Hull: 400
Armor: 2600
Evasion: 10
Speed: 100
Cutholoid
Cost: 3700 Minerals
Size: 8 (Battleship)
Mutations Size: L
Natural components: 4x Large Meteroid Slinger, 1x Huge Devouring Maw, 1x Regenerative Hull Tissue
Hull: 800
Armor: 4500
Evasion: 5
Speed: 80
TIYANKI
Energy Siphons are an energy weapon with +100% damage vs shields and -75% damage vs armor and 60 range. Tiyanki are overall the toughest space fauna, but have a weak innate offense and low speed. They do well with mutations that add an anti-armor weapons, but unfortunately they get a reduced benefit from Maneuvering Tentacles (biological afterburners) due to low base speed. Good on defense, but the slowness is annoying.
Space Whale Hatchling
Cost: 550 Food
Size: 1 (Corvette)
Mutations Size: S
Natural components: 3x Small Energy Siphon, 1x Regenerative Hull Tissue
Hull: 500
Armor: 200
Evasion: 25
Speed: 80
Space Whale Calf
Cost: 1100 Food
Size: 2 (Destroyer)
Mutations Size: M
Natural components: 3x Medium Energy Siphon, 1x Regenerative Hull Tissue
Hull: 1100
Armor: 300
Evasion: 20
Speed: 80
Space Whale Bull/Cow
Cost: 1700 Food
Size: 4 (Cruiser)
Mutations Size: L
Natural components: 6x Medium Energy Siphon, 1x Regenerative Hull Tissue
Hull: 2400
Armor: 500
Evasion: 8
Speed: 80
Space Whale Ox
Cost: 3300 Food
Size: 8 (Battleship)
Mutations Size: X
Natural components: 6x Large Energy Siphon, 1x Regenerative Hull Tissue
Hull: 5000
Armor: 1500
Evasion: 0 (-100%)
Speed: 80
VOIDWORMS
Spikespores are missiles with 100% shield penetration and high hull (but not quite as high as Swarmer Missiles) and 90 range. Voidworm Fangs are an extremely short range weapon that doesn't have a type (kinetic/energy/explosive), but has +100% damage vs shields and +100% damage vs armor. Their speed is on par with amoebas, but they're a little weaker defensively, though they can grow to a larger size. They are the fauna best suited to be equipped with missile mutations, since they already have 1-3 natural missiles. They'd be really good, except there is a mismatch between the size of the adults and the size of the components they use. With all other fauna size 4 gives you L sized mutations and size 8 gives you X sized mutations. This might be a bug or it might be intentional, but in any case it means adult voidworms are only half as strong as they should be given how much naval cap they use.
Voidworm Nymph
Cost: 250 Food, 250 Minerals
Size: 1 (Corvette)
Mutations Size: S
Natural components: 1x Medium Spikespores, 1x Small Voidworm Fangs, 1x Regenerative Hull Tissue
Hull: 400
Armor: 0
Evasion: 70
Speed: 100
Voidworm Juvenile
Cost: 500 Food, 500 Minerals
Size: 2 (Destroyer)
Mutations Size: M
Natural components: 2x Medium Spikespores, 1x Medium Voidworm Fangs, 1x Regenerative Hull Tissue
Hull: 800
Armor: 200
Evasion: 35
Speed: 100
Voidworm Adult
Cost: 1600 Food, 1600 Minerals
Size: 8 (Battleship)
Mutations Size: L
Natural components: 3x Large Spikespores, 1x Large Voidworm Fangs, 1x Regenerative Hull Tissue
Hull: 4000
Armor: 1000
Evasion: 10
Speed: 100
Voidworm Troika
Cost: 4500 Food, 4500 Minerals
Size: 16 (Titan)
Mutations Size: X
Natural components: 7x Large Spikespores, 3x Large Voidworm Fangs, 3x Regenerative Hull Tissue
Hull: 12000
Armor: 3000
Evasion: 10
Speed: 100
Edit: Forgot to mention quality. Quality is a general modifier that is used to increases the stats of your fauna. It progresses from Common to Rare to Epic to Exceptional. I can no longer check in my game what Rare quality does, but Epic fauna gets +20% to hull, armor and shields and +10% to weapon damage, evasion and sublight speed, while Exceptional fauna gets +30% to hul, armor and shields, +20% to weapon damage and evasion and +15% sublight speed. As you can see the bonuses get quite substantial.
Edit 2: Added info on Voidworm Troikas.