I was going to do more of an essay but then I went into quite a bit of detail in the patch notes. So here's the notes:

• Fleet Combat: Now with 'Overlapping Waves'
  
  • Instead of fighting to the death before new ships can reinforce, both factions can now build ships on a cooldown known as the Warp Coil. The Warp Window is open when the Warp Coil is charged, and if the game is paused the player is able to warp in as many ships as they want before the Window closes. Once closed, the faction must wait for another Warp Coil recharge to buy more ships.
• New Ships:
  • Striker: A front line upgrade to the Militia with a focus on offense
  • Gunship: A front line upgrade to the Striker, though a bit slower and less maneuverable
  • These ships were meant to fill-out early game options for the player and add more Crystal-free offensive options.
• Armor Changes:
  • Damage can no longer 'pierce' armor. Armor must be at zero to do damage to a ship's HP.
  • Armor Value ship stat removed. All armor is now equal in value, ships just have different amounts of it.
  • Fighter armor generally reduced, Frigate and Capital ships are where you find a lot of armor.
  • Weapons now do a percentage of their damage to armor. For now Vulcans do 20% damage against Armor which makes them feel significantly weaker against armored targets. Other weapons generally do OK against armor, with Missiles and Torpedoes probably being the biggest value Armor-wise.
  • These changes are an attempt to set up a bigger distinction between early game fighter mobs and later game Capital ships and heavy fighters. Militia and Scrubs now get shredded in the late game, and Capital ships now have a much longer life expectancy against swarms of Vulcan users.
• Repairs in Combat
  • Engineers and Paladins now do their repairs in the heat of battle. With less free time between skirmishes, these ships were barely doing any repairs so now they can do them on the fly.
• General Balance:
  • Pirate ships have been made generally weaker, most especially in the early game. Scrubs, Goons and Underlings should all feel a little more flimsy. Enjoy it for now, I think the Federation might be due for some nerfs soon.
• Documentation:
  • Tutorial and in-game Manual updated with new combat mechanics.
• HUD Changes:
  • Various features added to inform the player about Warp Coil status.
  • Tool-tips added to non-interactive elements like resource counters.
  • Added 'cannot afford or otherwise make this' sound fx.
  • Changed the HUD's font, I think it's a lot easier to read now but I don't know what others think.
  • Several minor tweaks and changes all over the UI like usual.
• New Music:
  • Thanks to soundimage.org for the tracks!
  • Added some mood variations for clearing a level and defeat.
  • I understand that these music files seemed to boost the installation size quite a bit. I will look into compression.
• Bugs:
  • Fixed: Higher tier Pirate ships were spawning way too early in some cases.
  • Fixed: Clicks on Time Controls sometimes don't register.
  • Fixed: Game stats on the end of game screen were way off.

In the near future perhaps: Some new Research, new Pirate ships, new ways to obtain Research and Research Points, and perhaps some more player ships with more 'utility' and/or an economic focus.