After SF2 Revival, I always thought there weren’t any outstanding conflicts, assuming you threw the obviously what-if endings out the window. Yeesh.
Eh, so far, I don’t mind many of the changes in the comic, itself. Ken being already married to Eliza basically just means there won’t be a love story of him falling in love with Eliza early on as far as I can tell. Well, okay, sure, I suppose it also means it might dodge a “Ken leaves Eliza to participate in SF2 for a while” thing, but that story can be done with Guile and his wife, anyways
Whatever happens to Cammy, though, I’m a bit more interested in, but I think there’s a misinterpretation or something when Udoneko said Cammy would work for Bison first. The storyline discrepancy here would be Cammy working for Bison during SF2, since Udoneko said the comic would take place first during SF2, but I believe that since then, the comic storyline’s been changed to take place during Alpha first and Udoneko forgot to mention it, what with the thing starting off with Gouken being killed and all. Besides, I think having Alpha be a flashback would be a very VERY bad idea. There are TONS of characters in Alpha that will be very difficult to have another character flashback to. How the HELL will Birdie, Karin (unless Ryu flashbacks about her, which would be silly), R. Mika (unless they’re going to devote a section to Zangief flashbacking about Alpha, which would also be silly), the Dolls (unless they make Cammy regain her memory somehow, which would really @#$@# with her mind. …well, okay, I suppose you could have Vega/Balrog flashback it but that’d be kinda weird, I think), and and basically EVERY Final Fight character (since there are no Final Fight characters in SF2) have a decent storyline role in a flashback? For you to flashback to the past, someone has to REMEMBER the past, and there are tons of storylines in Alpha which are not very connected to SF2 at all, only very loosely connected, or connected in such a way that those involved would not remember it. Alpha’s storyline is too friggin’ BIG to just be a flashback. It’s probably the largest most complex part of the SF storyline (33+ characters in Alpha 3 alone each with their own stories and sets of mid-bosses and such would guarantee that). It has to be shown in it’s own light, unless Studio Udon and Capcom Japan want to either cram it into too small a space or have a flashback that takes up more issues than the actual present itself.
…so anyways, yea, I’m thinking the comic now starts in Alpha but Udoneko just forgot to mention that, which would get rid of the Cammy working for Shadaloo during SF2 discrepancy because now she’d be doing it during Alpha. 
Being out of the loop regarding the comic industry, I don’t really have much to say about Maduriera. But if Udoneko knows Maduriera in person and as a friend, that’s going to make it a lot harder for Udon to criticize the guy both in public and in his own mind, I imagine. The human mind tends to bias itself in that way, so I don’t think it necessarily has to be a comment to try to get the comic to sell so much as Udoneko sincerely believing that because he knows Maduriera as a friend thus biasing his mind towards Maduriera.
Heh, I don’t have to be blunt and possibly undiplomatic regarding the canonity of the SF comic. Udoneko was kind enough to give me his own paragraph about it to copy and paste in that thread. 
Regarding Shotosatsukan: I’ll say it again. Whatever. I’ll change/clarify the thing if it isn’t, already, but that doesn’t mean I’ll actually CARE. :o But then, the plot guide has a lot ofpaltry details in it that I don’t really care about but had to include for the sake of completeness, anyways, so that’s nothing new. Before I actually upload a new update, though, I’d like to see if I could possibly (and subtlely) get more clarification from Udon regarding his statement about alternate parallel universes and blah. It may or may not be a big deal, so I’ll go ahead and update anyways if I can’t find anymore info on it, but I like to at least try a little and give these things a little time before going on and uploading a new version. 