If I were a betting man, regardless of behind the scenes claims, I'd say the reshoots were the fairly cheap to realise (a fence, four speaking roles and some sheds) pre-credits sequence in North Korea that had nothing to do with the rest of the film and was immediately followed by what felt like another pre-credits sequence with the bomb raid.
The only real thing that suggests it might have always been there and wasn't just added to put that bit more Tatum in is it fits in surprisingly well with the rest of the movie's attempts to homage Die Another Day as much as possible (the rescue the hostage by shooting them bit being the most subtle).
Other than that, a good fun film that suffered (possibly because of bits being cut out to keep the running time the same after the new scenes) from characters popping up out of nowhere with very little explanation. Or indeed, as with the case of most of Joe's OAP friends, not to be seen again with very little explanation.
Highlights included Firefly- I didn't know he was going to be in the movie and not only was he well done (thankfully in a film that took a lot from the comics most of his Hama created backstory- of the "Oh yeah, he's also a ninja who was involved in the death of the Hard Master like it turns out everyone else in the book happens to be and he can also move his head so fast you can't photograph him" variety- was ignored) but I liked the misdirection over who it might be with the introduction that made it look like we might be getting another Dreadnok. Or I suppose the first as Movie Zartan seems to not even like bikes.
It was also really cool how the Mummy came back in what was effectively a non-speaking cameo as well (though again, one confused flashback scene suggests he might have had more that was cut).
Willis and the Rock were good solid fun (though the former could basically sleepwalk this and wasn't in as much of the film as his prominence on the posters suggests) but Lady Jaye and Flint were, whilst harmless, completely bland. The later to the point they might as well just have reused Scarlett.
The real fun is to be had with the villains though. As mentioned, Firefly was fun, and Jonathan Pryce- despite looking somewhat frail- got to have a whale of a time hamming it up brilliantly as effectively the main villain. Cobra Commander was basically wasted but looked fantastic if nothing else. And no attempt to impersonate Chris Latta either, which was nice.
I liked the Bill Paxon-ish prison warden as well, it was a nice touch that despite being an immense dick he wasn't completely inept when Storm Shadow and Firely performed the jailbreak and actually got a couple of hits in. I wonder if they got Eccles back in to play popsicle Destro
If it has a really big flaw (beyond typical dumb blockbuster things like the President can suddenly announce Cobra as a nice government agency as if no one has heard of them before yet the US have a guy called Cobra Commander in prison and Snake Eyes and Storm Shadow seem to be international celebrities), anyone who doesn't really know their G.I. Joe is going to have the fuck confused out of them.
Not only in terms of how closely it follows up the first one but in that you really need to have attended the Larry Hama school of Ninja to understand large chunks of what's going on in the Snake Eyes plot.
The Blind Master is one of the guys who just sort of turns up and I don't think there's even the slightest explanation of where all those Red Ninjas who are so loyal to Storm Shadow came from. And for a film that tried surprisingly hard to follow on from the first it completely ignored his death as well.
Also, of course, they should have had Duke go into a coma.
That quote above makes it sound like a lot more than it actually is. 
