The third series of Doctor Who is a great run of episodes that would quickly become classics, though a lot of hate is directed at Freema Agyeman for simply being the companion to succeed Billie Piper. If you look at the character of Martha Jones subjectively, she's a good energy to have around the TARDIS and her chemistry with David Tennant is pretty good. I don't think she deserves the negative reception and some of her episodes are some of the best in the show's entire run.
Series three featured the heartbreaking two-parter "Human Nature" and "The Family of Blood," which saw the Doctor transform his DNA into that of a human so he could hide from a dangerous alien family. This new human named John Smith remembered nothing of his true self and thought he was a real person. These episodes were extremely well-written and showed a truly vulnerable side of the Doctor and the people who are affected by him. We also saw the first appearance of the now iconic Weeping Angels in "Blink," which guest-starred Carey Mulligan as investigative reporter Sally Sparrow. Of course, the epic three-part finale is what made series three memorable, as we were finally treated to the return of the villainous Master.
The three-parter, "Utopia," "The Sound of Drums," and "Last of the Time Lords" sets up the resurgence of the Doctor's most dangerous enemy, the Master, played briefly by Derek Jacobi and then prominently by John Simm. The twist in "Utopia" is still one of the biggest shocks I've received on this show and stands as a shining example of the incredible writing that's always been the cornerstone of Doctor Who. David Tennant's second series is definitely a winning one and looking back, it's no surprise why he resonated so much with fans.