Where to start...Okay. First up the storyline, I knew from reading online and from the gundamoffical forums as the show was airing in the States that it was a re-imagining of the original series. What with the boy finding gundam scenario, aided by the destruction of the colony, then the legged ship (trojan horse in the original series). Of course the big changes was the fact there was now more then one gundam, something which all series G onward have had (Turn A is the exception but i think Tomino was able to stop people wanting it full of gundams, he never did care too much for the toy side of things afterall), the storyline between Kira and Athrun and the masked character being a genocidal manic.
Now I don't mind re-imaginings or remakes...as long as they are good and can prove their worth over the original. The only plot line that they did add that that i liked really was the whole rivalry between Kira and Athrun, which ended in one of the best fights of the whole series (including Destiny). My main problems would have to be they didn't do enough different and a lot of it was cliched (or at least i thought so) half the time i knew what was going to happen and when people were going to die. The whole Rau thing as well i just thought it was silly, his motivation for destroying eveything? because he was a clone wow that sure beats everyone else's motivations, I mean how can Char's stack up to that, or even Ulube from G Gundam?
Another thing is n-jammers, a very poor plot device, they seemed to be SEEDs answer to minkosy particles from the original series and the way of stopping nukes and long range combat and what have you. That would be find if it wasn't for the fact that they are then underminned by having N-Jammer cancellers, which only serves as another plot device (oh look we can use nukes again! we're going to nuke ZAFT while they use their Gigantic Space Weapon(c) on us). It would of been far better if they just took the minkosy particles wholly from the original series and just left it by that.
The characters didn't help matters either, Kira was just a big doormat who kept sprouting the same nonsense towards the end, is it so wrong to expect another Kamille or even Loran? You can see why he gained the nickname "Jesus" since he's managed to pull off some serious miracles thanks to plot holes (Really I'll buy the Astray explanation of Kira's survival from his fight with Athrun, that's far more likely then anything else)
Lacus...was just too...fantastical? I like my female leads strong for the first part of the show she just came off annoying and then in the latter half I didn't buy her at all as the leader of any sort of group. Also i know this isn't the show's fault but it always irked me that they had two voice actresses for the english dub of her, it couldn't of been that hard to just get one who could sing as well.
Flay, I already named her as one of my most annoying characters so i'm leaving it there.
Athrun, a likeable character, more likeable then the main star. He also had the best pairing on the show, shame the director didn't like it since it was sadly crushed in Destiny.
Cagali, a better female lead then Lacus....You know what i would of liked SEED a lot better if Athrun and Cagali were the stars and Kira and Lacus were supporting them.
with regards to the animation, I found the mix of CGI mech and traditional stuff to be jarring especially on some of the archangel shorts, and the character designs were not my cup of tea, but that's something this shares with S-cry-ed. Also i disliked the heavy use of flashbacks which grew more commonplace as the series got on (Yes i get it, Nicol and Tolle are dead, i don't need to be told a hundred times!)
Music wasn't too bad but wasn't anything to write home about in the wake of more recent efforts (like the first two Gundam 00 ops)
Now onto the most important aspect:
The mechanical designs
Strike was a nice design on its own, although the pack system did mess things up, seemed like from that point on all the backpacks could only get bigger.
The other four gundams to start off with had some nice aspects, Blitz mainly, Aegis looked a mess and for a transformable one, a poor effort compared to designs like Zeta and Wing Gundam.
Justice looked, to me at least, plain and bland the backpack (again far too big) didn't look right to me. Freedom on the other hand, I confess this is my favourite design from SEED and in face it ranks in my top 10 designs of all time, it looks nice with its wings spread out and the colour scheme suits it well. Sadly they had to turn it into Strike Freedom but oh well.
I think that wraps up my comments on SEED, I won't bore you with my critisms of SEED Destiny but i can sum them up for you: Flashbacks, Main Character Swapping, Finale, Co-ordinator favourtism and stupid pairing choices
Of course i should probably add this disclaimer to that little rant:
These are my opinions, i'm not saying they are fact, this is just what i believe.
EDIT: Maybe i should read through it next time to make sure that spoilers aren't in full view -_-