This. 5 and 6 are my favorite. Well written, full if mysteries and discovery, some if the shows best music and awesome doctor speeches and encounters and twists... I could go on...
Yeah, the music, the speeches, and the Silence, the story archs, everything, it felt like Doctor Who reached its peak then. My thoughts on each series:
Series 1: Difficult to judge this series in retrospect. It's very dated and often absurd, it doesn't take itself as seriously - Aliens of London - but on the other hand it's not often dull and it's now classic. The Ninth Doctor and Rose as characters, and their relationship, work. The Parting of the Ways finale is epic and emotional. Moffat wrote the best 9th Doctor story, no surprise. I think this is one of the better early seasons.
Series 2: Tennant's a great Doctor. Rose was the perfect companion for him and the other two were in her shadow. Unfortunately they didn't have many good stories together. As with Season 1, the best episode is Girl in the Fireplace, which is a perfect episode for 10 but doesn't involve much of Rose. Second to that is the two Satan Pit episodes, one of the best Tennant (and Rose) stories. School Reunion was good, with Sarah Jane. Tooth and Claw and The Cybermen introduction is alright. Then there's some really bad and meh episodes, like Fear Her, Army of Monsters, The Idiot's Lantern. It's mixed, with higher highs and lower lows than Series 1.
Series 3: Probably worse than Series 2. Martha was a good companion and she had one of the best introductory episodes, but the rest of the series didn't live up to the opening. The Daleks in Manhattan episodes were awful and the finale with the Master although it started alright ending over-the-top in its ridiculousness. The Shakespeare episode isn't bad, the Human Nature duology is pretty good, and obviously Blink by Moffat is a classic.
Series 4: I'm not a fan of Donna and there were a lot of terrible and boring episodes, excluding the Fires of Pompeii which is one of 10's best. As per usual, Moffat wrote the best story of the series, Silence of the Library. The finale is epic and a great reunion with all the characters, but also absolutely absurd, towing a planet. Of the specials, only one was great - Waters of Mars - and the End of Time had some good moments.
Series 5: This is where it really takes off. Matt Smith and a full Moffat takeover. The speeches. The theme. Amy. The Eleventh Hour is the best Doctor intro, and it has other gems like the Angel duology and Vincent and the Doctor. It probably has the best Doctor Who finale too, The Big Bang is epic and not absurd like RTD's finales.
Series 6: Maintains the momentum very well through the excellent two-part opening in America. Peak Doctor Who. The rest is mixed but rarely bad. Its ambition is admirable. The finale is anticlimactic but probably comes off better binge-watching it and still manages to feel epic. I like A Good Man Goes to War.
Series 7: Mixed. The worst episode of 11's time is by the new show runner, Dinosaurs on a Spaceship. It gets a lot better when Clara takes over, I love The Snowmen and Bells of Saint John. And I think this was Clara at her best. 11's theme gets even better. The finale leads into an epic and absolutely major story for the Doctor which will be difficult to top.
Series 8: A lot of promise. Deep Breath was fantastic and set a completely different tone for the show and the Doctor. Peter Capaldi's great. Listen's great. Unfortunately his and Clara's relationship was kind of awkward and Danny Pink was the worst mistake of the series. It's better than any of RTD's series.
Series 9: The best Doctor Who writing since Series 5? Maybe. The two opening episodes with Davros and Missy are among the show's best episodes ever. The duologies were a good idea. A great speech from Capaldi's Doctor for once. Capaldi's guitar playing. Heaven Sent is possibly the best episode of the series with the best twist ending. Clara's exit is emotional. The finale with the Time Lords is epic but unfortunately leads into...
Series 10: Which seems to have totally lost the momentum from that finale. It's alright. It seems like it's getting better. But so far, it's not compelling. It's at the bottom of my rankings.
5 and 9 are the best.
The main difference between 6 and 7 is that 6 was an ambitious series that didn't come together, whereas 7 was a profoundly unambitious series that didn't come together.
7 unambitious? Nah.
It begins having each episode be like a short movie with high production values, it introduces a companion who starts as a mystery and by far had the most impact on the Doctor's life, and it sets up the end of the Doctor's life cycle with the huge event that was the 50th anniversary episode. It's more ambitious than S6 was.