90 minute route

Beating the Game requires the Mu'kay trial, The Codes from the Phasymt, and their pre-requisites.
The optimal weapon that is still "accesible" is the 16,000 RU Heavy Dumbfire.
Fleet ships are mostly used to safrifice so you can flee from battles.

Solar System -
Get the Ship parts from Mars and Neptune before talking to the Alien so you only have to see him once.
Rescue the Alien and kill the Scyve - This should de-spawn the probe so you don't have to fight it too.
Return to Earth for Hyperdrive
I hit Titan now since I might have to reset over it if the "wind" memes me.
Three Favors - 
* This stuff needs re-routing the MOST
Activate the space station. (I put this one on the auto pilot list since it's used a lot I don't have to fiddle around with mouse cursor later)
* Visit Tywoom Homeworld - Doing it early advantage= Extra Tywoom Defender if you get random Kzanti or Scythe(transport) attack you in Mukay space= Doing it later= Better placement of the free refuel
Visit Mu'kay Homewold - You can do save researcher before being asked, but NOT Ice world or colony missions (Ice world needs a visit and Colony mission beaten)
Activate Mu'kay Space Station (I don't add it to auto-pilot list since you only return here through the fast travel interface and not normal flight)
Go to Save Colony in Lacaiie 8760
Hit Planet Wastear and Planet Vistaver for 5000 RU and a sellable item worth another 5000 RU
Go to Alpha Wendigo - Get the Free Hyperdrive on Alpha Wendigo 1. Record the Ice Planet
Approach Wendigo Space Station from the left to refuel to avoid dialog with the Tywom
Buy Lander Cannon and equip the hyperdrive (Far faster than the Lexite Sidequest method)
Go to Delta Horos planet 2.
You can't see the animal from space, but it IS visible during the falling animation, head for it immediatly, but if it did move, leave and drop again to reset his position.
Go to Beta Chaudhary to pick up crashed ship for trial later
Turn in Mukay Homeworld quests - You need the money since combat will start in next section.
*
Go to Tau Ceti (If you auto pilot from Earth's Space Station you are fine, but if you auto pilot from Mukay homeworld you should manually steer to avoid going through Scrthe random encounters)
Purchase the Heavy Dumbfire Misssle
Go to Alpha Xiplohs Space Station.
* If money is pushed even thinner then you could get here and do the Trandal stuff before the Pinthi to use that combat money.
Buy the cheap Fuel Tank (The Flagship energy charger will be bought here on forced revisit)
Go to Alpha Acroix - Manually fly left a little to avoid MenkMack]
Ally Pinthi
Teleport to Alpha Xiphlos Space Station
Go to a Trandal area that has at least 2 ships in it (preferably more)
*You could land on Eta Corpus to sell the Hyperdrive(20,000). Money 
Make sure that you DO NOT talk to the same trandal twice in a row, you will lose the ability to Fire at Will and the kill them to ally quest
Make sure that you DO NOT leave a system without Fire at Will at least one Trandal, or you will lose the ability to do so.
After you talk to one Trandal, Fire at Will one of the others (if it's a 2 ship group instead of 3 ships fire at will another one (NOT the one you talked too)
You will receive the Mu'kay Trial message now.
Talk to one more Trandal to ally with them.
Go to Mu'kay homeworld
*Pick up the Trandal ship on Beta Chaudhary if you didn't do it earlier)
Go to Tywom Homeworld (Trandal don't give dialog option to identify the item before this point)
*Talk to a Trandal - if already allied you can use the one ship at EARTH.
Heal NOW to skip the boss entirely
Go to Mu'kay homeworld and go through the trial dialog
DO NOT VISIT EARTH
Teleport to Pinthi and Fly to Beta Ishikawa
Do Phaytmid Homeworld Dialog
DO NOT VISIT EARTH
Refuel at Space Station and Fly to the Xrathi Place
* If you are incredibly low health, you can avoid all combat by getting ~4 Tywom
Unleash the xrathi
You can now visit Earth without Triggering the boss fight.
You will need the 2nd Fuel tank to do the Evil Pinthi quest
*First + the Special Module from the Drenkend Space station would also work?
*Maybe using a Melnrome Trader to refuel mid way would also work
Enter this star system from the bottom side so you are right on top of the planet you need to land on.
Go to Earth to heal (bad ending would be faster but...)
Get to final boss

To do List - 
Change order of stuff in Mukay area
Ally Trandal before Pinthi (to prevent running out of money)
Double Check to see if NotCudldle Drive + Hyperspace Module lets you avoid certain Scrvthe/Xrathi Ships
Fly to Evil Pinthi area from Pinthi space station instead of Phaymid to avoid enemies?
If you ever finish a fight with less than 6 health use the autosave to go back.
Check to see if Trandal can be allied with less conversation.
Check to see if Phaymid Flee strategies are worth the time dialog takes.

Minor Tech
Unlike Star Control 2, you cannot run away from battles as an escape key action.
However, after either killing the first enemy in the group OR sacrificing a minor fleet ship, you CAN Flee.
Running away via this sacrifice method almost always works in Hyperspace, even enemies that can outchase you will let you go since the "stun" period after fleeing lets you get out of aggro range
Running away while within a Solar system works if the enemy is about to despawn via event (First visit to Xrathi) or you only have to cross about 1/4 of the screen before leaving (Evil Pinthi research). Otherwise you will probbably need to run away from them twice.
Only Two ship types should be considered - Tywoom and Pinthi.
Mukay Area - Ideally only the Drenkend fight should be done, but Scyve Freighter and Kzanti seem to get in the way about 2/3 of the time. These are easy fights, but you can't really run from them, they can attack again after an escape with impunity.
Trandal    - Most have bad AI, but the multiplayer ship (Trandal Frigate)will sometimes abuse your bad turning and it's frame-based damage can leave you on very low health (remember healing will be unavailable after the trial if you want to skip the first boss)
Phymtid    - Well known during casual playhtroughs, They're still mean here. I think buying the first turning upgrade before flying to them is worth it. Generally less dangerous at long-range compared to short range.
Scythe     - Heavy Dumbfire can obliterate them, including the Battlecruiser from multiplayer (It won't get a chance to turn unless really lucky with it's spawn location)
ScytheDread- These are worth Sacrifice Fleeing from. If you use Pinthi for this instead of Tywom, they will deliberately aim away from you and you'll have to do most of the damage by ramming the outer arena. Can be killed by the Flagship, but kind of awkward, and slow.
Xrathi Hyperspace - You no longer need money, so Heavy Dumbfire the first one and then flee.
Xrathi Origin Area- Killing the first in a group and then using Flee makes it VERY hard to avoid the "Friendship cutscene" 
Origin     - On normal difficulty using FLagship the entire time isn't that bad, but Pinthi are still faster at breaking the sheiid. 
Origin     - You don't need to get close to it, but in practice attempts I actually bought Point Defense during the last starbase shop - the black hole momentum can throw you closer when you aren't expecting it sometimes.

You can enter Star Systems from different directions. This saves time, and helps to avoid combat in the case of (Evil Pinthi Lab)

When you go fight the Origin, you can avoid the "friendship" cutscene if you run at it without stopping. Fleeing from Xrathi on the way instead of killing all 3 can mess this up because you have to "push" the Xrathi out of your way

If you do not visit Earth after the Mukay Trial AND complete the first visit to Origin, the Scythe boss event will be removed.
The Xrathi Fleet Boss things can be completely ignored in the context of the speedrun, although you might get message about the Earth one being close during the Pinthi-Origin Flight.

Outdated stuff
If you do fight the Scythe Boss on Earth, Dumbfire is strong enough to face tank him.
I originally thought that whole Drenkend thing was mandatory.
The fights are doable with 3 Tywom and Fly straight through the entire thing, Drenkhend Homeworld, Picking up Menkmack, and getting the helmet. You will run out of fuel/rescue to teleport back afterwards.
This was all done before purchasing the Dumbfire Missles (Getting the Free Advanced Nuke was originaly for this and it was sold AFTER I was done using it)