My first Doctor was technically Jon Pertwee, since the first story that I ever saw was "Spearhead from Space." But the next several that I saw after that were all Tom Baker stories ("The Robots of Death" & the 6 Key to Time stories). It wasn't until I saw the Doctor & Romana bickering at the beginning of "The Ribos Operation" that I actually started to like the show.
Now, my favorite Doctor is probably Paul McGann, with Patrick Troughton as my favorite from the classic series and Peter Capaldi as my favorite from the new series. (But then, most days, William Hartnell, Jon Pertwee, & Tom Baker are all at least kinda in the running for favorite Doctor as well.)
As for ranking the seasons from the new series:
1. Season 5. I love the Smith/Amy/Rory combo (with bonus points for every episode with River too). The story with the cracks was a simple, unobtrusive arc that made sense at the end yet still tied into a few other episodes in major ways. It's also got several of the greatest episodes of the series-- "The Eleventh Hour," "The Vampires of Venice," "Amy's Choice," "Vincent & the Doctor," "The Lodger."
2. Season 6. It's still Smith/Amy/Rory (with a lot more River this time), so it gets a lot of the residual goodwill that I have towards Season 5. There's a couple great episodes, like "The Doctor's Wife" & "The God Complex." But the stuff with River & Amy's pregnancy & the Silence & the Doctor's death all get way too convoluted.
3. Season 8. I love Peter Capaldi's Doctor so much. Granted, Season 8 sometimes struggles with episodes that work a bit too hard to make him act like a jerk ("Into the Dalek," "Kill the Moon"). But this season makes the best of the Capaldi/Clara chemistry and hits many high notes with "Deep Breath," "Listen," "Time Heist," "The Caretaker," "Mummy on the Orient Express," & "Flatline." I also love the bickering between the Doctor & Robin Hood in "Robot of Sherwood."
4. Season 9. "Heaven Sent" is a masterpiece. "The Zygon Inversion" features the Doctor's definitive anti-war speech. "Under the Lake"/"Before the Flood" has some great timey-wimey aspects while also being a great base-under-siege story. "The Girl Who Died" is an episode that I found underwhelming the first time but was really blown away by on repeat viewings. However, the scene is dragged down by convoluted crap like all that stuff about "the hybrid" in "Hell Bent" and the indulgent continuity porn of pointless episodes like "The Magician's Apprentice."
5. Season 7. This one's hard to rank because it's really 2 separate seasons. You've got the first 5 episodes saying goodbye to Amy & Rory and then the last 8 introducing Clara & the mystery of the Impossible Girl. But either way, there aren't really any great episodes within the season itself. ("The Day of the Doctor," while great, is a special and I do not count it as part of Season 7.) Still, I like Matt Smith and I prefer Moffat's more humorous Doctor Who over RTD's more angsty take on it.
6. Season 3. As has been said, it went through a really rough patch in the middle from "Daleks in Manhattan" through "42." (We could lose those episodes in a 1970s-style wipe and I wouldn't shed a tear.) But it does hit some high points towards the end with "Human Nature," "The Family of Blood," & "Blink." The 3-part arc with the Master is also pretty good until you get to the end with Jesus-Doctor.
7. Season 4. Admittedly, this is the season that I have probably seen the least often of any of them. I like Donna but she rarely gets a chance to shine on her own since most episodes are also bringing in another companion like Martha, Rose, or River. Season 4 does include my favorite RTD episode, "Midnight." I'm also a sucker for large crossovers, so the big Doctor Who/Torchwood/The Sarah Jane Adventures team-up at the end is a huge hit for me. On the other hand, "The Doctor's Daughter" is a really tough episode for me to get through; too much shouty-Tennant.
8. Season 1. In retrospect, it feels like a really early experiment. The show isn't quite sure how outrageously outer-space-y it can go yet. Eccleston's Doctor, while fitting the concept of a Doctor still freshly bearing the scars of the Time War, kinda feels separate from the other Doctors both before & after him.
9. Season 2. After Eccleston's moody, shell-shocked Doctor, David Tennant's energy was a breath of fresh air. The show also finally starts to embrace its outer-space-y roots in a bigger way with alternate universes, black holes, and base-under-siege stories. On the other hand, Tennant & Rose get way too gooey with each other, there's too much running down corridors being chased by unconvincing CGI monsters ("Tooth & Claw," "School Reunion"), and this season also features 2 of the worst episodes of the entire new series: "Love & Monsters" and "Fear Her." (I used to think that "Love & Monsters" was the worst thing that Doctor Who could ever do. Turns out Sylvester McCoy's "Delta & the Bannermen" is even worse but "Love & Monsters" is still a close second.)