Why do my bosses all have minimal defense?

Solution 1:

Here's a description of how to evolve bosses from a Jay is Games commenter:

First, you need to understand how to grow parts.
To get Wide, you need to get horizontal extensions.
To get Attack, you need vertical extensions.
To get Armor, you need to attack the guns in close combat.

Now the parts that will be created:
Wide top = Wings
Wide bottom = Arms
Attack top = Buster
Attack bottom = Striker
Armor top = Tornado
Armor bottom = Defender

Now the evolution flow.
Pure Heart = The first ship, and the base and foundation of the rest of the ships.
Intial forms:
W=Wide, A=Attack, M=Armor
Pure Heart + Top part + Bottom part
PH+W+W=Double Wider
PH+W+A=Wide Attacker
PH+W+M=Wide Armor
PH+A+W=Attack Wider
PH+A+A=Double Armor
PH+A+M=Attack Armor
PH+M+W=Armored Wider
PH+M+A=Armored Attacker
PH+M+M=Double Armor

Evolution 1 forms
Double Wider > Wing Arms
Wide Attacker > Wing Striker
Wide Armor > Wing Defender
Attack Wider > Buster Arms
Double Attacker > Buster Striker
Attack Armor > Buster Defender
Armored Wider > Tornado Arms
Armored Attacker > Tornado Striker
Double Armor > Tornado Defender

Evolution 2 forms
Wing Arms > Asura
Wing Striker > Pheonix
Wing Defender > Hammerhead
Buster Arms > Scorpion
Buster Striker > Muramasa
Buster Defender > Big Magnum
Tornado Arms > Hekatoncheir
Tornado Striker > Berserker
Tornado Defender > ISE-ONE*

Evolution 3 forms
Asura, Pheonix, Scorpion, Muramasa > Infinity
Hammerhead, Big Magnum > Catastrophe
Hekatoncheir, Berserker > Armageddon

*ISE-ONE no longer evolves into a third form.

That's a bit hard to visualize, so here's a nifty chart showing evolution through tiers 2 and 3: