I found it again.  OK, a couple of thoughts come to mind.  
On the whole, this strikes me as the ultimate new character fic.
Is there a reason why the Knight Sabers need to be a part of this,
when all of the other characters are so godlike that they could 
crush the KS, or their opponents, like insects?  

I just love the casual way that Kurumi tampers with Nene's mind for her 
own convenience.  The staggering arrogance of a god-like being indeed.
Oh...and Kurumi?  I'm sure your sister appreciates the way you do the 
absolute minimum required to take care of yourself and Nene, and let the 
A.D. troopers do their own dieing.  

       What happened would forever etch itself in Nene's memory.
       Too bad she wouldn't be remembering it for long.

These statements are mutually incompatible.

       "There is a saying that evil could never be truly destroyed," 
Sylia
replied in a clam manner.

Sylia is so shellfish.  

     The four startled Knight Sabers whirled around to face a hulking
silver boomer that towered over them by a good four feet. It was 
massive,
larger than anything they had ever encountered before. Its red eyes
glared at them as it stood there not a hundred meters away, leaning on 
a
pillar, arms crossed.

Then the pillar collapsed because of all the structural damage, and boy 
did the Dreadnought feel silly.  

Incidentally...Dreadnoughts?  What's next, the Sentinel series of 
boomers?  Say...Deathlok would fit pretty well into Mega Tokyo...
Genom doesn't make shiny silver robots though.  They clash with 
the city's esthetic.  

       She mentally chided herself. Genom had always been trying to 
kill
them. Not that they were successful at times.

Hooey.  If Genom was trying to kill you, you'd be dead. Still, I suppose 
nothing keeps Sylia from having delusions of grandeur.  Incidentally, 
that last sentence doesn't make sense.

       Leon sighed. "Kyoko, what the hell are we doing?!! Why are we
arguing like kids while boomers are out there killing everything and
anything??"
 Kyoko shrugged, sticking her tongue out. "I dunno."
       "Maybe it's the world coming to an end," Leon muttered.
       "Just what was that again, big brother... hmm...?" she purred
dangerously.

...What are they talking about?  I can't make any sense out of it.  

     "So what?! You tried countless times. I already killed five of 
your
number. If you want to kill me, then come on!!" Kyoko challenged.
       With that, Kyoko summoned her own crystal and cried out.
       "Tek Sector!!!"

Uh...yeah.  Well, you already said you were changing this.  But doesn't
it seem just a bit on the coincidental side that someone happens to be
setting a massive trap for the Knight Sabres, just as someone else is
hunting their runaway cyborg of fantastic power, while a left-over Tendo 
of godlike powers just happens to be flying into town?  Maybe Skuld 
should do some debugging.  

It might work better if Kyoko is forced to use her powers against the 
boomers, giving away her location to her pursuers so they can show up 
next chapter.

     Two minutes later, the boomer was quite agile and had proven a
difficult target to hit.

Given the physical description, a lot of agility seems relatively 
unlikely.  

       "Perhaps you should wear something, miss. The night is cold and
standing her in the gardens naked even though no one is around is quite
improper for a young lady," a soft, motherly voice told her, the tones
mildly reprimanding.

If no one was around, no one would be talking.  In fact three people are
around.  

     "There is no need for you to worry. I highly doubt any of them
could be a match for me." Kyoko blinked, wondering just how powerful 
was
this woman. "I know how that sounds, but it is the truth. You do not
fight Teknomen as long as I have without managing to gain power." 
Nodoka
smiled. "Come now, you are tired and must rest for the day."

What appalling arrogance.  She deserves to get her butt polished.

     "You don't have to worry about him. He's sleeping now and will 
not
wake for at least a few hours. The draught I gave him for his pain will
take care of his injuries," answered the woman named Kasumi who Kyoko
felt could be trusted.

What draught?  You didn't actually write her giving him anything.  

Over all...I found a feeling of pointless, random exercise of power 
about this.  It feels to me like all these crossover elements were just
tossed together with no real goal in mind except escalation.