*In the beginning, I would have made it clearer why Shang Tsung is fighting Liu Kang's brother Chan at the Shaolin monastery before the tournament has even begun. Maybe we could see Chan at dinner with the other monks and hear Shang Tsung whispering taunts and challenges telepathically. He manipulates Chan into accepting a challenge and after beating and crippling him but before he claims his soul, he tells him that now the monastery has no champion and Earth will fall to Outworld. In the actual movie he seems to be telepathically taunting Liu (all the way from China no less), even though later on he studiously attempts to avoid fighting him. Here there will be no deliberate attempt to provoke the more capable Liu and it would show just how much of a mind-screwer Shang very early on, in a thoroughly terrifying way, rather than having Raiden tell the audience this and only show it at the very end (when he takes Chan's form in the fight with Liu).
*The revelations Shang makes in the process of beating on Chan will reduce the need for Raiden to explain everything to the main characters later. During the podcast, Raiden got referred to as "Basil Exposition" at least once. I didn't mind, but moderation in all things...
*Speaking of Raiden, if I could find an Asian (or at least more "exotic" looking) actor who can deliver as well as Christopher Lambert, I'd have cast him. When Raiden arrives at the temple, his features obscured by his conical hat, and it's revealed he's a white guy in a wig, a lot of my podcasting friends just started laughing. If he physically resembled the game character more, that would've been better. The stuff the character does will pretty much stay the same (besides the reduced exposition), as I liked Lambert's Raiden.
*The scene where Sonya and Jax raid the nightclub in search of Kano will be a bit more realistic. Kano's henchman will actually fire his gun properly (rather than holding it Gangsta Style) and at least some people will notice there's a gunfight going on. Yes it's a mosh pit and I would imagine a lot of the people are high as a kite on something, but nearby gunfights tend to sharpen the mind. Kano could escape in the hubbub and Sonya could pursue him to the docks...
*When Sonya chases Kano onto the scary dragon ship taking the contestants to the tournament, I'd have made Jax a heck of a lot more emotive about it. His partner's running into a situation that could get her killed (or something less lethal but still unpleasant, given how this is the first time Shang Tsung pervs on her). He's trying to stop her, but he doesn't sound remotely invested in it at all. If I were in his position I'd be screaming my head off.
*I would keep Cary Hiroyuki-Tagawa for Shang Tsung, but whenever he has to make a big loud pronouncement, I would use SFX to amplify and deepen his voice. If it's too blatantly different from his actual speaking voice, hang a lampshade on this--it's an invocation of his supernatural power, much like the Gou'ald voices and eyes in the Stargate universe.
*Practical effects for Reptile--a big puppet in the style of Pumpkinhead or (some of the time) the Jurassic Park velociraptors. He looks like a video-game character and the CGI has not held up well. The whole chameleon-invisibility thing was done pretty well in Predator, made years before this one, so using CGI for that alone and physical effects for Reptile could have been awesome.
*When Liu Kang fights Kitana, I would make it clear there's a lot of hostility between her and Shang Tsung. It should be clear Shang is trying to make her fight Liu as an act of sadism (although we won't know just why until later) and Kitana simply refuses to give him what he wants (Liu Kang's death). When Shang tries to point out the rules require the match end with a death, she points out the rules were made by someone higher on the food chain than him, a reference to her adoptive father Shao Khan and hinting that by being too harsh on her, he risks his master's wrath. This aggravates Shang, who orders Liu to fight Sub Zero immediately even though he might be tired from dueling the superior Kitana (who, being 10,000 years old, is almost certainly a more skilled fighter).
*The Liu and Sub Zero fight will occur as it did in the film, only without Kitana there to remind Liu of what to do and Sub Zero's ice shield not taking forever to form. This would strengthen Liu some, as he'd have less help and remember what he's supposed to do on his own.
*When Art Lean faces Goro and Goro defeats him, it's Johnny Cage (who has actually interacted with him) who freaks out first. Sonya, who doesn't know Art well, doesn't freak out until Shang Tsung sucks his screaming soul right out of him. Given how the film hints at romantic interest between the two of them, this shared freak-out could be a bonding moment. In the actual movie it was reversed, and that didn't make sense.
*I'd leave the fight between Johnny Cage and Goro--and the prelude between Shang Tsung and Johnny Cage--as it is. It sets up the climax rather nicely.
*Sonya's abduction by Shang Tsung was pretty pathetic in the movie. I would depict Shang panicking when his champion Goro is killed by Johnny Cage and immediately order his minions to kidnap an unprepared Sonya and drag her off to Outworld so he can fight her there. Rather than her implied but not seen pathetic showing against Shang in the film, we see her getting mobbed by dozens of ninja minions and have her put up a decent fight. She could even defeat these two featured-extra minions who we see shouted at each other during multiple fights but never get any particular explanation.
*In the movie when Liu figures out Reptile is stalking them and attacks him, Reptile is somehow incorporated into this man-eating statue alongside the road in Outworld and transforms into a being resembling his video-game incarnation. He proceeds to have a lengthy, brutal fight with Liu Kang...while Johnny, who is nearby, does nothing. Given how Johnny, Liu, and Kitana infiltrate Shang Tsung's tower in Outworld dressed as monks, perhaps a bunch of them attack Johnny while Reptile engages Liu and he has a fight with them?
*When Kitana joins up with Johnny and Liu and reveals her reasons for being an ally to the Earthrealm characters, someone should raise the obvious question about why exactly she's allowed to undermine her father's plans by aiding the Earthrealm warriors in the tournament. After all, she might be some kind of double agent. As part of her revelatory spiel about how Shao Khan killed her parents and adopted her, she could claim that Khan allows her and Shang to screw with one another on the grounds it keeps them from plotting against him or that her little rebellion amuses him. Johnny Cage could even drop some one-liner about how if she helps foil Outworld's designs on Earth, "he won't be so amused now." At that point Kitana might look afraid--being a Rebellious Princess can have a price.
Alternatively, the video games depict her rebelling against Khan after learning she isn't really his daughter, but in the movie she seems to be opposing Shang's plans from the first time she appears. If we go with that, she can mention this as something she found out just prior to the tournament and she made a beeline for Earth immediately. This way Khan won't know she's turned traitor...until he does. Shang can be as hostile as he is in the canonical movie, which would show that he's smarter than his master.
*When the final duel takes place, Shang should adopt Chan's form, which discomfits Liu to the point Liu can't fight him. Shang will not have this problem and will beat on Liu until Liu summons the courage to renounce his guilty feelings for his brother's death at Shang's hands and attack Shang-Chan, beating the tar out of him and then fireball-punching him onto the spiky floor below. He can then transform back into Shang Tsung as he dies, freeing all of the captive souls he's taken.
*I would make it clearer just how Our Heroes managed to escape Outworld after Liu killed Shang Tsung. I'd have a bunch of minions show up to kill them (perhaps some really scary ones, to show how dangerous Outworld's armies would be if they actually invaded), only for Kitana to pull rank as the princess of the Outworld and tell them that Earthrealm has won this tournament and the victors are to be escorted back to Shang Tsung's island immediately. In the movie we never saw how they escaped from Outworld and got back to Liu's monastery and that was kind of an issue. Plus the coming of Shao Khan could be foreshadowed by having his telepathically whispering ominousness in Kitana's ear as Liu, Johnny, and Sonya leave rather than the blatant (and kind of ridiculous) sequel hook/cliffhanger we got in the canonical film."This victory is only a temporary setback and you will not be able to foil me again" (or something to that effect). Kitana immediately sets off after the Earthrealm warriors.
*When we see Johnny, Liu, and Sonya (and Kitana too, making it clear she has abandoned Outworld) at the Shaolin monastery being congratulated by Raiden for their victory, everybody's back in their proper clothing. It would have taken days for them to get there and I would imagine Sonya in particular would have wanted to get rid of the BDSM slave Leia outfit and put her hair back in order as quickly as possible. Compare her preferred appearance to this. If they want to do the obvious set up for Mortal Kombat 2: Annihilation, the scary thunderstorm can start and it ends with Raiden whispering, "The Emperor." No need for a mediocre CGI sky-monster there. Save him for the sequel.