Here are a couple of things that I feel like the audience takes for granted as true:

1.  The three killers Moriarty hired to kills John, Mrs. Hudson, and Lestrade are actually hired to kill those three. 

Now, we can infer with near certainty that the sniper who disengages after Sherlock's fall was assigned to kill John.  I'll take that.

But we never see the same with the police mole and the bald-headed fix-it man (with the gun in his tool box) -- how can we be so sure that these two were Moriarty's men?  Could they have been hired by Sherlock?  We don't ACTUALLY know or have closure that these two men got the call to "stand down," so how do we even know that there were supposed to kill Mrs. Hudson and Lestrade? 

Which segues to the next....

2.  The international hitmen were hired by terrorist cells, and Moriarty had a hand in all of it, and/or they had the primary purpose of getting the computer keycode. 

During Mycroft's and John's meeting, Mycroft says "If it's not Moriarty, then who?"  

That should be a tip-off that things may not be what they seem.  They may not be hired by Moriarty, or have any interest in Moriarty at alll.

There's a possibility that it could be John, Sherlock, or even Mycroft who hired those hitmen, to protect Sherlock -- and they had no intention of recovering any sort of key code (even though it was mentioned by the last killed hitman). 

John could have hired them to protect Sherlock.  John was a captain in the military, he probably has the connections to procure international hitmen.  Plus, John was not scared or impressed when presented with the information of the foreign hitmen -- if anything, John was rather ambivalent.  He wasn't surprised that they were there, or surprised about who they are.  Why?

Sherlock could have hired them himself.  Sherlock has proven himself capable of infiltrating terrorist cells -- perhaps he struck a deal to get protection?  Or, he could have hired them to fool Moriarty into thinking that there are terrorist cells who are interested in Moriarty's key code.

Or, it could even be Mycroft who hired them, since we know that he feels guilty for setting Sherlock for his eventual purported demise by blabbing to Moriarty. 

Or, maybe Mycroft hired them (by offering them pardons/releases for their cooperation) to obtain the alleged keycode that Moriarty left to Sherlock.  Remember, Moriarty got on Mycroft's radar in the 1st episode of S2, then he was detained and interrogated at the end of the 2nd episode, and in the 3rd episode, he is revealed by Mycroft that he had been interrogating Moriarty for something, something extremely important. 

So, maybe Mycroft hired these assassins to try to get the "key code" from Sherlock?

Basically, there's a lot more to these international mercenaries than we know.  From what we're shown, they're just mercenaries who are interested in some key code that Sherlock received from Moriarty.  But should we so readily accept this as true?

Again, the big tell is Mycroft asking (paraphrasing) "If they're not Moriarty's men, then whose men are they?" 

3. Sargeant Donovan is clean, and other than Lestrade's assassin, Moriarty has no one inside Scotland Yard. 

However, what if Sargeant Donovan is one of Moriarty's accomplices? 

We know from the pilot that her morals aren't exactly squeeky clean (since there are strong hints that she gave Anderson a, um, gift that requires scuffing of the knees).  And perhaps she's showing compassion in trying to convince John to keep his distance from Sherlock, just to avoid any collateral damage caused by Moriarty's wrath. 

We also have a scene in The Great Game where she receives a call from one of Moriarty's Semtex hostages, and she hands it off to Sherlock.  Perhaps Moriarty instructed the hostage to call Donovan's phone, a number which he already has?  Sherlock already has the pink phone at this point -- why does he need to be contacted via Donovan?

Also, Donovan WAS the catalyst for raising suspicion that Sherlock might be a fraud.  Donovan not only pointed out the mathematical impossibility of Sherlock's Addlestone feat, she may have said something to the kidnapped victim girl that caused her to scream when Sherlock entered (e.g., "we caught your kidnapper, here he is..." or something else). 

Donovan was the gatekeeper between the children and the others -- how can we be sure that we know everything that the children said or didn't say?   Who knows?  Maybe the girl had further things to say that would have exculpated Sherlock (i.e., explain the scream), and Donovan didn't report anything; maybe Donovan had a role in the brother's unconsciousness. 

The bottom line is that Donovan could have been commanded by Moriarty to raise and maintain that element of doubt, and the most important thing to control is the testimony of the brother and sister -- since the testimony would tell EVERYTHING.... but we don't get past the gatekeeper, Donovan.  Coincidence?

Donovan was also the first to find the children -- even before Sherlock -- which means that Donovan was either extremely lucky, or she was faster than Sherlock, or she already knew where the children were hiding, via Moriarty. 

These are all just possibilities. 

LASTLY, and I am CHEATING here....

I'm going off-canon for "evidence," but Vinette Robinson, the actress who plays Donovan, has been cast in a pilot by NBC for the upcoming 2013-2014 schedule. 

Does this mean that Robinson's character, Donovan, meets her demise in Series/Season 3? 

Of course, she could work on both shows.  However, it'd be tough having a 24-episode series shooting in the U.S., then shooting 3 "films"/mini-series episodes in England).  I don't even know if that's logistically possible, even for her minor Sherlock character.  The more likely explanation, in my opinion, is that Ronibson's Donovan is arrested for her work with Moriarty.

Once Sherlock resurrects himself, I'm assuming that he'll go on hell-bent path to ID and capture all of the guilty parties, including Donovan.

4. John's cabbie for his ride back from checking in on Mrs. H was nothing out of the ordinary. 

We remember John getting the call from the "paramedics" that Mrs. Hudson was critically shot, and then he promptly makes it to 221B to check on her.  After assured of her safety, and realizing that it was a ruse, John grabs a cab ride back.

We see John run across the street to the cab, and he even shooes away a potential cab-rider (who might also be a Sherlock accomplice).  In order for Sherlock's jump to work, we pretty much have to rely on John's altered and perfectly-positioned point-of-view of Sherlock's jump. 

There are so many different spots where John could have been dropped off, which would have ruined John's point of view of Sherlock's jump (at a different corner, somewhere closer or farther, etc.).  The cabby didn't even drop John directly in front of Barts, but at the perfect spot -- presumably as planned by Sherlock -- for John's final call and Sherlock's final "note." 

So, perhaps Sherlock's planning goes as deep as the perfect cabby for John's return to Barts.

Anyway, these are just some "facts" that may very well be proven to be untrue/opposite/different in the upcoming season (or series).  I know I thought of more, but can't remember them for right now..... but I'll add if I remember them.