There's a few reasons I think there are more secrets in this game than we know about.  A great deal of them (probably all) have been found out and posted: the fatalities, stage fatalities, babalities, secret fights, etc.
 
However, after playing the Challenge Tower mode excessively, I've experienced several things.  I've fought zombies.  I've fought AS a zombie (not an existing character with red eyes and grey flesh, but a zombie with his own move set).  I've fought as Goro.  I've fought as a movie director.  I've fought a black armored robot named Unit 5 as Reptile, and after that, I was fighting Cyrax and Sektor in green robot armor as Reptile.  I've also fought against who they called "Inferno Scorpion" I think., an awesome looking alternate costume for Scorpion where he has many wounds and no mask, revealing his "true" face: just a skull that's constantly on fire (now THAT'S the Scorpion I wanna use).
 
I've googled a lot to try and find out if I can unlock any of these extra costumes like Cyber Reptile and Inferno Scorpion, and if I can play as Goro or a zombie, etc., but I've had no luck.  I can only find the secrets I was already aware of.  Given Ed Boon and any MK game's love of secrets and unlockables, don't you think there would be even more secrets especially if they're being sort of hinted at in other parts of the game?  
 
I can think of a few explanations.  The first I hate to admit, doesn't seem that probable, but it may be possible that there some secrets so cryptic that hardly anyone besides the creators know about them so far.  That's a little far-fetched though because even though this game is pretty new, we have an army of hardcore gamers across the world dedicated to finding secrets aggressively, and it's hard to believe someone had missed any so far, or that they weren't leaked by someone at least.
 
It's also possible that there ARE more unlockables, but Ed Boon hasn't made them available yet.  Maybe a future update could add more secrets over time (maybe without even letting us know) so we'll all really be thrown for a loop.
 
OR, maybe extra unlockables were included in the existing DLC packs, like if you download Skarlet or extra alternates you may also get more stuff to find out.  Yet it seems more likely that these wouldn't be secret if they came with DLC, but rather mentioned in the description to give people more incentive to buy, or at least a sentence mentioning there are more secrets but without giving away what they are exactly.
 
OR, speaking of DLC, doesn't seem too far-fetched that some future DLC will just be packs of secrets that you download.  It seems like something Boon might do, because before the internet, you would learn all the secrets from your friends or arcade challengers, and they would spread by word of mouth.  That seems like something people might miss, not knowing every little secret right away, but figuring them out over time, it hearkens back to when arcades were still a thing, an element that would fit in with the incredibly nostalgic tone of the game.  Boon loves having secrets in his games and prefers to have people work for and salivate over the things they have yet to discover, that's pretty obvious, so it doesn't seem too crazy that they'd release packs of secrets later which would basically amount to Boon saying "here guys, have at it."  
 
Then again, it doesn't seem too smart to ask people for money for something when they don't even know what they're getting, either.
 
Those are my theories regarding the nature of secrets in Mortal Kombat games.  I'd just like to know that there could be even more unlockables out there.  I mean, I've bought every single item in the Krypt and even found all the secret chests, yet I still don't have an alternate costume for Kratos, which I know exists by the way.  Also, I still don't have Jade's second fatality (I'm aware I don't need to unlock it to do it, but I found it strange that it wasn't in the Krypt).  And even after buying everything in the Krypt and it told me I'd bought 100% of the chests, there was still one more extra chest in each area of the Krypt.  So for example, in the Blood Marsh area, it says I've bought 84 out of the 83 items there, so it's possible there are even more hidden/extra chests.
 
And what the hell is up with the Krypt monster that pops up every now and then to scare the shit out of me?  There has to be something going on with that...whenever I see him pop up, I try pressing multiple buttons very quickly to see if it will lead me to yet another secret, but no luck so far.
 
The fact is, MK9 has spoiled me.  It has more to offer than basically any other fighting game right now, or even in the past (except smooth online matches), and therefore it just makes me crave more, especially when it definitely seems possible they exist.  I'm way more of a Street Fighter guy myself, but I can't stop playing this game...and as you can see, I've become fixated on the secrets...which explains the endless speculation.
 
What do you guys think?

There are enough people out there who dig through code that I doubt we are missing anything. Also, assets are so expensive to produce these days that making something cool and hiding it away is a pretty dumb move.

Those are just one-offs for the tower. The disc code has been thoroughly dissected, I doubt there is anything left to find.

I wouldn't be blown away to see Cyber-Reptile and/or Cyber-Smoke bundled together in a future DLC package, but beyond that, I'd bet we won't see anything more come out of the Challenge Tower. It's more for novelty anyhow.

Well, it's not exactly a secret, but I just learned today that there's a hidden achievement for performing every character's Babality.

I agree with the "guys who digs through code would have found it"-part...
 
Another interesting thing that are in the game but not accessable are:

Hidden classic characters actually have their respective classic move-set (Reptile having Sub-zero/Scorpion specials, Jade having Kitana/Mileena specials and Smoke having Scorpion specials). Personally I'd love to goof around with these characters... but I figure they are just broken and unbalanced.

Well just about everyone that cares has already tore the game apart literally digging through the code and the vast majority of players that is left would be playing online, leaving very few to find stuff even if there was anything left to find. 

 
But it did remind me of the time that someone found sound clips from SFIV, at least a few months after its release, of the announcer saying "Dee-Jay Wins!" and likewise with T. Hawk, hinting that they could possibly be in a future version of the game, and of course they were eventually in SSFIV.  I don't remember if they found these clips on the disc itself or through someone's twitter feed or something like that, but I guess my point is, regardless of how obsessive and diligent people can be in finding secrets, maybe something will arise later, but again I agree it's not very plausible at this point.  This post was, in a sense, just me thinking out loud, and just remembering Ed Boon talking in interviews about the importance of keeping secrets so people don't know everything right away.
 

I wouldn't be blown away to see Cyber-Reptile and/or Cyber-Smoke bundled together in a future DLC package, but beyond that, I'd bet we won't see anything more come out of the Challenge Tower. It's more for novelty anyhow.

@MysteriousBob said:

@Sir_Ragnarok said:

I wouldn't be blown away to see Cyber-Reptile and/or Cyber-Smoke bundled together in a future DLC package, but beyond that, I'd bet we won't see anything more come out of the Challenge Tower. It's more for novelty anyhow.

You do realise that 'Cyborg Reptile' is just a green Cyber Sub-Zero, right? I want to see more classic costumes before we get into stupid fan-fiction terrority.

With all of Reptile's standard moves, yeah. I still wouldn't be blown away to see it.