... you know this is The Impossible Question, right?
(WARNING: The following contains spoilers for all three seasons -- except for the series finale of series three, because I don't know how that one ends anyways. But for the rest: BE WARNED!)
I can say this, at least: Season Two was _not_ my favorite. I find that I prefer Rose Tyler with Nine than with Ten -- after all, what initially drew me into the series was the relationship between the characters, as played by Billie Piper and Christopher Eccleston; and, while I have actually come to think of David Tennant as "my" Doctor, it's still Rose and Nine that I best love to watch together, not Rose and Ten. (And I must add this: I am SO GLAD that Rose was seperated from the Doctor when he was Ten, because, as painfully, awfully horrible as that was for Ten to lose Rose, I don't know that Nine could have ever gotten over it. Or, at the very least, it would have been too horrible for ME to get over watching the Doctor, as Nine, lose Rose. Ten's Doctor obviously loved Rose just as much as he did when he was Nine, but, to me, there seemed more ... emotional interdependence on Rose when the Doctor was Nine. Which you can argue is a bad thing or a good one, but I'm getting WAY off topic. Forgive me; it's been a *wild* day.)
(... I also enjoyed Rose's character journey more in Season One than in Season Two, though she definitely develops in both; but again, let's not go off on another tangent, right?

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So, while there are a lot of good Season Two episodes that are my favorites -- New Earth, School Reunion, The Impossible Planet/Satan Pit, and the beautiful Love and Monsters (not to _mention_ the special The Christmas Invasion, oh oh *oh*!)-- it is definitely not my favorite season. I get stuck, however, trying to choose between Season One and Three.
Season One is the season that made me first fall in love with the Doctor; it's the one season where we're given Eccleston's Doctor; it's the season where we meet Rose (not to mention Captain Jack Harkness!). However, I have _really_ liked a lot of Season Three episodes a *lot* (Smith and Jones, The Shakespeare Code, The Lazarus Experiment, Human Nature/The Family of Blood, Blink, and of course Utopia and The Sound of Drums, and I bet that The Last of the Time Lords will join the list when I FINally get to _see it_. Oh, and the Christmas special, which I've only seen once and really need to watch again -- was awesome, even if this one _didn't_ quote The Lion King). I really like Tennant as the Doctor, and I agree with you when you say that it's in Season Three that he really comes into his own. The character development for the Doctor has been fan*tas*tic, consistantly so, and I fell in love with Martha's character at long last in The Sound of Drums. ("I'll _do what I like_!") And the bringing-back-of-Captain-Jack was just _perfect_, oh so perfect on _so_ many levels ...
But Season One! My introduction of the Doctor! CHRISTOPHER ECCLESTON! _AND_ ROSE!! And my all-time favorite episode, "The Parting of the Ways!"
... alright. Season Three is my favorite, and I'm voting for it. But Season One, when I met the Doctor for the first time -- "Hello, Rose Tyler.
Run for your life!" -- will *always* have a special place in my heart.