Seems like the Intel reveals lots of information, have you had the chance to read all of it?

So far i have actually read none of the Intel data base, was just too much text for me. However, I might read all of them soon enough to catch up with the storyline.

they even dropped the cheesy lines like

"peace through power"
"in the name of kane... kane lives in death"
"one vision, one purpose... the technology of peace"

You're not going to find an argument from me if you think that the C&C 3 story isn't impressive. However, there are a few things I think are relevant:
1) The Scrin are taking orders from someone else. This seems relatively clear in the Scrin campaign, but I cannot recall any support for it in past games. Now, the EA response to this rather unexpected turn is probably that it was going to be in the story all along. I don't know how true that is.
2) The Scrin technology--namely, the tower--is something Kane wants his hands on. The ending implies it is something he could not get otherwise.
3) This does not fit with the fact that "Kane did not steal the [Scrin?] ship--he made it."
4) The explanation for the lack of many mutant forms in C&C 3 is that Tiberium kills quickly. This means that it is not the alive mutated humans that the harvesters want; it is something else.
5) You say that Kane was "given alien technology to extend his life so he could spread Tiberium". I find that interesting. This implies that Kane was an agent sent (or recruited?) and that the transfer of that technology took place thousands of years before Tiberium came to Earth (if you link Kane to Cain in something more than name, and if not, he still appears in Red Alert).
6) If Kane is an agent of an outside force that's not the Scrin, he can only be an agent of the Scrin's commander, yet if this is the case, why is he confused and hostile to the Scrin?
7) I am quite certain that EA held a "story summit" at one point prior to the release of C&C 3 that included discussions among some community leaders in an attempt to fix the plot. I would like to know in more detail what transpired there, but it seems no one is talking about it.
8) It is my belief that EA was slightly uncertain as to where to go next and unwilling to take the C&C story in a bold stroke. With C&C 3, they played it quite safe, simply introducing characters and depicting the Scrin invasion. With C&C 3's expansion I think more of what they think is the proper continuation will come out. My guess is that they didn't want to risk serious backlash about the story in addition to backlash about everything else (simplistic gameplay, bugs, etc).
9) The story written for Tiberian Dawn, Tiberian Sun and Firestorm was the story conceived by Brett Sperry in the early 1990s. He was forced out by EA during the Westwood takeover and there remains at EA no person--in my view--who was intricately involved with the original creation of the story. Louis Castle, who is often labelled as the founder of C&C, said prior to Westwood's closing that C&C was always Sperry's domain. I don't trust him like I would trust Sperry.

I love the Tiberium game series, but ive never found the story impressive to be honest. Its just a complete copy of the Dune series, which Westwood originaly used to make (Dune, Dune 2, Dune 2000, Emporer) and of course westwood got the story from the brilliantly written Dune book series. The whole harvesting tiberium idea came from the harvesting spice off arakis, a powerful substance used for time travel and used to prolong life, and which 3 super powers fought for control of (Ironicly the nice but powerful Atredeis team which is exactly the same as the GDI (Including mechs, huge tanks, carryalls, snipers, and minotaures which are nearly the same as juggernaughts, sonic tanks(towers?)), the evil and merciless Harkonan with their vile leader (whom also love flame tanks and nuclear missiles, flame troopers, etc), and the slimy but strange and futuristic Ordos team (whom use alien like technology and forcefields, laser tanks which look like the devourer tanks, and whom also use Thailaxu which are beetle like creatures). In my opinion I think all the credit should go to the Dune story, because the Tiberium story was completely inspired from it if you ask me. So many people I know celebrate the whole Tiberium story like a relegion, yet if I ask them about Dune they say they have never played it or never liked it. There is one thing ive noticed about Tiberium wars, and that is that it is very similar to Emporer:battle for dune. The red zones often have you building your bases on cliffs, like in dune. The blue zones are all nice and green and lush, and belong to the GDI, EXACTLY like in Dune, where Atreides had control of Caledon, there beautiful lush planet, in which Harkonen also tried to conquer. And of course the whole buidling refineries and harvesters to harvest tiberium is from Dune, where you built Refineries and harvesters to harvest Spice (which also spread like tiberium). I still like the story of Tiberium wars alot, but I think much more credit should go to the Dune series.