Honestly, Christopher eccleston is my all time favourite. I think Cappaldi steals the second place spot, with David and Baker following. I realy didn't like Matt smith, he was good in his first series but he got too childish, he didn't seems like a 1000 year old genius. Though that's not his fault, he didn't write the scripts. Christophers series set the tone best, it was also genuinely frightening and it seemed like the characters were actualy under threat. While this trend continued with David it stopped with Matt. Alot was done that realy shouldn't have been done. For instance, bringing back most old villians. The Daleks, for example, haven't been very threatening. In Eccleston's series and Davids final series the Daleks were truly formidable foes, powerful, evil. With Eccleston they were insane, worshipping their emperor as a god, they were made of humans and they killed alot of people, including main characters, ultimately they felt like an unstoppable force, that required either wiping out the human race to defeat or time itself. Then in the stolen earth episodes we had these formal daleks, powerful and apart of an empire, with enough power to destroy everything. Then we had daleks who
A. Who planted a bomb on earth and attempted to create a new race of Daleks, they were actleast worthy of being daleks
B. New supreme Daleks who let the old Daleks plan run, turned on London's lights and ran away
C. Attempted to save the universe by locking the Doctor away
D. Asked the Doctor to open some shields so they could kill their own kind
E. Daleks who got owned by the doctor as he was dying
F. Fought some soldiers
G. Invited the doctor to meet Davros, get regenerated and be destroyed
Although the adventure games did them justice
Honestly, that's not to say they didn't have potential, but I feel they should've gone with the twisted, last of their kind route and build up to some point where there's a new Dalek empire, and have them act rather than do nothing. Also they shouldn't have shown how the angels move, kills the effect.
However, there have been some great enemies, especially in Capaldi's series. The return of Zygons, Ice warriors and Silurians have been great, and having the master create an army of Cybermen is fantastic. Again though, some shouldn't have returned or shouldn't have returned like they did. Also if you haven't watched Bad Wolf/Parting of the Ways you should, realy shows the tension I'm talking about.