To reiterate what everyone else has been saying seasons 1-2 were FANASTIC. seriously even better than lost at times.
Season 3 was good in different ways. Lauren as a one time addition was great. However Vaughn became insufferable and boring as a result, a different guy from what he used to be. His charecter really went downhill from then.
Season 4's stand alone episodes were a waste of time in my opinion. I thought Nadia was a meh charecter until her backstory was explained. That one episode was pretty beneficial to her charecter developement. But I did not like the "end of the world/zombie" plot in Russia and besides, zombified Nadia should of died in the finale, not spend half the next season in a coma... Also the fight which explained the symbol should of dragged on for at least 5-10 minutes. The Faux-Francie/Syd fight was longer and more epic than that and the nadia/syd fight was plain disappointing.
I don't understand what purpose Dixon served after season 3. He should of died an heroic, sacrificial death sometime before season 5 (perhaps Tom could of came in in season 4). And I was pretty fed up with no one thanking Marshall ever (even after he saved Sydney from the coffin in "Tuesday") or treating him like a normal person especially Vaughn (who reached new levels of arrogance/intolerablility in season 4).
Season 4 went downhill and so did Season 5. I don't think any enjoyed having the plot lines being recycled continously like having Sark/Irina/Sloane escape at their own convience, Sloane being evil/then good/then evil/then good/then evil, Irina and Syd being cloned, etc.
but the last 6 or 7 episodes were GOLD (except the series finale). however the way Alias ended was too mild and lukewarm. The murky explanation of Rambaldi/the Horizon was not sastifying. Rachel/Tom's ending was beautifully done (I really hate how they recycled that plot in LOST ) Tom's witty comments made the season more enjoyable and I didn't think he was a bad charecter at all.
I really would of liked the writers to have explained Peyton's backstory more including her true motive for being a villian. I guess we're supposed to assume all villians are in it for money/power. Rene and her were both snubbed, they both could of received some sort of a fb episode. Hated that in the middle episodes they sort of abandoned fully explaining Rene/Dr. Decanstis and why the fake Rene's dad was in the box in the first place.
If I could rewrite the series finale, I would tie up Jack/Sloane's ending with the missiles. Instead of taking the predictable route of Vaughn/APO stopping the missiles, the writers should have written it so Vaughn couldn't enter the code in time so Marshall has to divert the missiles. Through radio communication, Jack and Marshall could have one last scene (who didn't find their scenes hilarious?) where Jack instructs marshall to send the missiles to his location in Mongolia. Then Jack and Sloane have that talk and the missiles hit.
Peyton should of escaped, then runs into Rachel who is unable to stop her. For Irina and Sydney, I hated how Irina ended up selfish and even willing to kill Sydney. I think the only way Irina could of redeemed herself was if she did get off the glass, then Peyton appears and shoots a bullet at sydney, but Irina pushes her out of the way, and takes the bullet, then dies. Sydney/Peyton fight then Peyton falls through the glass.
Along with the chinese torturer guy and will/danny making reappearances, I really think that would of been a very sastifying finale.