As I mentioned in the "Destro's Voice" thread, I skipped all the webisodes and just watched the whole thing on Cartoon Network last night.  My thoughts:
I'll mention what I didn't like first:
1.  Deaths:  Pointless, unnecessary, shock value.  Especially since Bazooka and Major Bludd were both killed 
off-screen within the first five minutes of the show!  There was no point to that other than to tell us that this show is for grown-ups.  I think the annihilation of Moscow would have made that point just as easily, without gratuitously killing off two major characters.  As Jay pointed out earlier, death in fiction serves a purpose, otherwise it's just death for death's sake.  However, although I disagree with Troopsofdoom on the inclusion of such deaths, I am in agreement with him that Storm-Shadow and Zartan could pretty easily be brought back.  Unfortunately, the same can't be said for Major Bludd and Bazooka, who were both autopsied.
2.  Some of the voices:  The problem was that they only had like five voice actors working on this thing!  Cover Girl only had one line, but she sounded like she had a Southern accent for some reason...?  It was painfully obvious in a few scenes that Steve Blum (Duke) was talking to himself as another character.  I was impressed, though, with Grey DeLisle as Scarlett, the Baroness, and Dial-Tone.  They all sounded relatively different from one another!  But -- 
what was up with Flint's "Batman" voice?!?
3.  Snake-Eyes vs. Storm-Shadow:  The fight was amazing, don't get me wrong; but it felt totally extraneous to the rest off the plot, and the flashbacks moved painfully slow.  I feel like that side-story could have been left out to let the rest of the story breathe a little more.
4.  Destro and the Baroness:  They came across as kind of incompetent.  That whole scene felt like something out of an episode of Sigma Six!  But at least they didn't die, I guess...
5.  The music:  Pretty much a non-entity.  I want music to pull me into a show, not lurk, unnoticed, in the background!!
6.  The abrupt ending:  That was it?  No wrap-up or aftermath?  And Duke's narration clearly said "On our return to the site...", while the read-out on the screen said "Honor returned to the site...", which, uhh... makes no sense.
7.  The lack of "Yo Joe!!"  C'mon, not even 
once???  I counted several opportunities where it could've been used!!
Surprisingly, that's about it.  Considering this thing was written by one of my least-favorite comic book writers, Warren Ellis, that's pretty impressive!  On to the things I 
did like:
1.  Some of the voices:  Though I felt that certain voices didn't fit, I really did like Steven "Spike Spiegel" Blum as Duke (though I obviously would've preferred the return of Michael Bell), as well as the voices for Destro, the Baroness, and Cobra Commander.  And the guy playing Snake-Eyes 
nailed that voice!  He sounded exactly like the original version! 
(Incidentally, Cobra Commander and Gung-Ho were both played by Charlie Adler, who also played Starscream in the Transformers live-action movie.  And all those characters were previously portrayed by the late Chris Latta.  Weird coincidence, or something more?)
2.  The animation:  Probably the very best 2D G.I. Joe animation ever!  It was fast, fluid, and gorgeous!
3.  The character designs:  For the most part, with the exception of Stalker's unfortunate hair, everyone had a very nice update of their classic look.  I would love a Resolute Scarlett figure!  Destro had an appearance very similar to his Sigma Six character design, I thought, which was not a bad thing.  On that note, though, I absolutely loved the Baroness's Sigma Six design.  I wish they could have carried it over here, too.  Also, Tunnel Rat's team seemed to be wearing outfifts that were a homage to the orange diving suits on the classic cartoon, which I thought was really cool.  Oh, and the 
Flagg looked really neat.  Too bad it blew up...
4.  Scarlett + Duke:  I am by no means a "shipper" (to use the technical term), but given a choice, I strongly believe Scarlett and Duke are a better couple than Scarlett and Snake-Eyes!!
5.  The overall story:  Except for the "more adult" slant, it reminded me of a classic Sunbow mini-series!  Cobra has some huge new threat, and the Joes have to split up, going to different spots around the world, to put a stop to it, before coming together for the big final battle.  Very neat!
In summary, though there were aspects I disliked, with the exception of the totally unnecessary killings of main characters, my other quibbles were minor.  I would love to see this become a regular, ongoing series, providing they either keep Warren Ellis away from it, or reign him in a bit.  Plus, if they could hire a few more actors (and throw in a "Yo Joe!" now and then), that would be nice!