Here's my quick grammar round-up, and a few other comments.

What if...?

Not quite sure what this title means. Did you just choose it because
it's incredibly general, or because you couldn't think of something
better? I think you need a bit more punch, and certainly more relevance
to the fic without giving a complete spoiler. Maybe a title in the style
of the series you crossed with....

Sylia stood at the window of the control
room and watched as her creations went through
their combat drills. She was amazed at how fast
they had completed their training.

how quickly, or how rapidly

It seemed like
they had been doing it for years instead of
weeks. Despite the fact that they came into
being totally by accident, Sylia was very proud
of them.

had come into being

*They are much more effective than the agents I
had chosen,* she thought, *I just wish that they
didn't look like....*

"Sylia!"

SYLIA: Yeah, that they didn't look like me. What was I THINKING? ...
They are kinda cute, though...

The shouting of her brother had interrupted
her train of thought. She turned to the door,
just in time to see Mackie come rushing in.

I think "Her brother's shouting" would work better.

"There's a rampaging boomer at the shopping
mall!" he said, "The ADolice have already
lost two squads trying to stop it and it
doesn't look like they are going to succeed
any time soon!"

ADPolice

"they are" sounds a bit unnatural. "they're" might be better.

As Mackie left to make preparations, the
Knight Saber's leader turned back to the window
and pushed the intercom button.

Knight Sabers', since there's more than one of them.

"Okay ladies," she said. "I want you ready to
go in five minutes. We have our first
assignment."

Many would put a comma into "Okay, ladies," but I think it's up to you.

As the shouts of joy came from her creations,
she couldn't help but smile. However, it
slowly faded when a single question surfaced that
she couldn't answer with certainty.

*I only hope we are ready,* was all Sylia
could reply as she left the control room.

That's not really a question....

    When they had arrived, Sylia could tell
that this would be harder than she thought.

You got them backwards. "When they arrived, Sylia could tell that this
would be harder than she had thought." Or leave "had arrived" if you
intend that to be in the past with regard to this scene, but I think the
past works better than the past perfect.

A large hole had been blown into the outside
wall. From there was a path of crunched
floor tiles from where the boomer had
walked.

Repeated "from" sounds awkward. I'd suggest something more descriptive,
like "From there, a trail of crunched floor tiles marked the boomer's
path as it wound into the mall."

Along the path, laid all kinds of
debris from destroyed storeowners, to smashed
benches.

Comma usage times three. "Along the path lay all kinds of debris, from
destroyed storeowners to smashed benches."

Poor storeowners... are they really destroyed rather than just dead?
Destroyed people sounds so edited DBZ.

After a few minutes of following the
trail though, they had found their quarry,
 a seven foot tall, silver, humanoid
figure throwing benches and other items
around at random.

trail, though,

And if you switched the first paragraph into the past tense, remove the
"had" from "had found" here.

Also she could make out
the shapes of some ADPolice officers had taken
cover at different spots in the mall.

Also, she

officers who had taken

I think "around the mall" sounds a bit better than "in the mall" here,
but it's not incorrect.

*A C-55,* Sylia thought as she watched the
boomer tear up some more railing, *It shouldn't
be too hard to defeat, I'll just sneak up on
it and...*

railing. *It shouldn't... defeat. I'll just...* (periods instead of
commas)

The only difference was that the
suits each had a different color scheme of
Blue, Green and Pink.

This sentence sounds really awkward. I suggest something more like "each
had a different color scheme: one was a pastel blue, the second was lime
green, and the third was a rather strong shade of pink." Use whatever
phrases you like, naturally.

"SURRENDER NOW!" The three shouted,"OR FACE THE
WRATH OF THE SABER PUFF GIRLS!"

Zing! We have a punchline. And as much as I'd usually advise you to end
with the punchline, the rest works very well in this story. See below.

All was silent for a few second then small sounds
of laughter began to come from the places the police
had taken cover.As they got louder, Sylia put her
hand over her visor and shook her head then
muttered:

a few seconds, then

I don't like the word "sounds" there... too bland. Maybe "small
chuckles" instead of "sounds of laughter" and then describe it building
into laughter in the next sentence. "As they got louder, building into
full-fledged laughter, ..." And while you're at it, the laughter is
coming from the policemen, not just from the places where they're taking
cover. "from the policemen who had been taking cover" is a bit tighter
there, and more descriptive.

You're missing a space between "cover. As"

head, then (need comma)

All in all, quite a good little piece. The punchline had me groaning a
bit, but since you didn't end with it, Sylia's reaction made a nice
wrap-up.

- Nidoking

LEO: I can't drive since my license got suspended.
HYDE: What did you do?
LEO: I dropped it in a glass of soda, and it just hung there, like,
suspended... then while I was looking at it, I ran a red light.

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