Replacing Space Crusade Aliens with something else

First, we need blips.

EBay Bingo Chips:
100pcs Clear Transparent Plastic Bingo Chips 1.9 cm - Green Price:
C $2.85

Stick white paper labels with the miniature silhouette and points value on one side of the bingo chip. You get a sense of "blip" from the green transparent plastic. I got 100 green and 100 red, so that gives me 3 sets of 32 green blips + 32 red reinforcement blips. I can have the original mix, a Ork/Kanz/Cybork/Cyborg ship. and a Dark Eldar ship with EM4 Mechs. Or whatever miniatures you have.
You could print copies of the original blips too of course, but the bingo chips don't require printing and cutting.

You might want to replace the Chaos Marines with Orks or Androids to reduce the species count. Or replace the Greenskins with Androids or Chaos Cultists.
Buy some weird minis on eBay and make blips for them:

The EM4 Mechs above are £5 for 10. So you can replace the greenskins with 10 androids, for a Chaos Android ship. Or replace the Chaos Marines with Ork Nobz, for an Orky ship, I can replace the androids with the Cybork above. Make up a movement allowance, armor value, Hand-to-Hand dice, and ranged attack dice. You can put the stats on the base, maybe 8,2,2 White, 2 Red for the EM4 mechs. Make up a point value to put on the blip. The total point value of the blips should be about the same as the original game. Make up reinforcement blips with a different label color (or transparent red bingo chips, which double as flame markers), with comparable points to the original game.

The ship will be the same, optionally separate the boards and add corridors:
Four 2x6 corridors would do. I have Space Hulk 4thEd, so the corridors are ready. You could print out new boards and make the originals double sided.
"Pathfinder Flip-Mat: Basic" is a plastic sheet of 1" squares (the right size) larger than the original playing area, so you could put the 4 boards on top of the Pathfinder mat and draw in the corridors.
 Here is my "Space Hulk Crusade" foamboard creation, with paper stats on the Starcraft bases:

No actual rule changes so far, just unit data. If I were going to have rule changes they would be:

Fluff: If someone is about to shoot you, but you are on a corner, you might be able to duck around the corner.

Rule: If you get shot and you lose a life point, and you could move 1 square North/South/East/West to be out of Line of Sight of the shooter, roll a die. If the result is 1 or 2, 1 lifepoint is instantly restored.

Comment: Hugging corners provides protection. So skillful tactical planning is rewarded. You can outflank your opponent so he has no place to hide.

Rule: Each Marine chapter gets 1 Overwatch token. Each Alien unit type (Grechkin, Ork, Android, Chaos, Dreadnought, not Genestealer) gets 1 overwatch token each. The miniature with the token may fire once during the turn of its enemy at any target that moves in its Line of Sight. If the target is out of sight after moving its first square, it cannot be targeted. Dreadnoughts may only fire their least effective weapon (Heavy Bolters) on Overwatch.
The token is placed beside one miniature at the end of the player turn, and removed when a miniature fires on Overwatch, or at the start of the player's turn.

Overwatch favors the defender, but also those with the most heavy weapons. If the Dreadnought got to fire all its weapons twice in one turn it would be unfair, so just the bolters.

If the above 2 rules are combined, the target of Overwatch can use the cover rule for protection.

Overwatch and the corners rule above provide a tactical puzzle in each combat turn, a bit closer to Space Hulk. So clever manoeuvre becomes as important as firepower in Space Crusade.

Weakest Link

On the campaign, if the least successful player is 2 ranks behind the most successful, they get promoted a rank to give them a chance.