The Silurians did not bother me too much. Definite costume change, they claimed they were not Silurians, but related, and then preceded to have a copy paste plot with both Pertwee's dealings with the Silurians. Both times Pertwee convinces the leader that peace can be made, both times things go terribly wrong and the colony is destroyed. This time Smith successfully convinces the leader and the leader ends up killing the rebels and forcing everyone else to sleep for I forget how long.
I've never read any of the novels, my opinion is only based off of things I have heard. That can be taken with a pinch of salt, I do not have sufficient research.
With the million year gap, how have humans changed? How have Daleks changed? How have timelords or most any other creatures changed? Very little, to have the Macra as the one exception going from being about the size of a horse to being large than sky scrapers was a bit too much. A name drop is not too much from Tennent, but he might also have just said, 'might these guys be related to the Macra?' Make a joke or something.
Tom Baker was very good at having new creatures virtually every serial. Daleks even got Davros as a nice addition. The Sontarons, introduced in Pertwee's final season, got another appearance, but not a reimagining. Same again in the Two Doctors. The Nu Who Sontarons kept the appearance close enough that I could easily recognize them as Sontarons. Sontarons were all about the strategem and having everything exacted out in Old Who. They were powerful and cruel. They were not, however, doing war chants and wanting to die on the battle field.
It's true the previous occasions were mostly scouts, the Nu Who could be a branch of Sontarons, a group directly from a war front or something, it's not impossible, I just did not think it was quite adequately explained for a number of the changes made. While this was 'good' mining from Nu Who, even getting a 'are you my mummy' as a nice joke, the newer changes just did not seem to make the cut. Just play it straight like the last x number of times, keep the Sontaron charm.
You're right in that each era changed. The first four Doctors really did good building on each other. For me, the Fifth Doctor was the first to break the chain. While he did reference things from the previous 4, he was unable to do anything with most any of them. Arc of Infinity had the reappearance of the Guardian with a rather goofy outfit and his plan simply did not add up to anything. Earthshock with the reappearance of the Cybermen was a disservice to them, same with Revenge of the Cybermen. More disservice to the Doctor though for the actions he took in the respective episodes.
Ironically, although Troughton is my favorite Doctor, many of his episodes I did not like the writing. I liked Troughton's ability to always be able to make good humor and get me to laugh at least once per serial no matter what was happening. A very talented actor, Jamie was awesome as well. Davidson and Matt Smith looked up to Troughton, just as Tennent looks up to Davidson as well. Though Smith's outfit is a lot more obvious than Tennent's glasses. I've seen a number of parallels between Nu Who writing and Troughton's era specifically, plot threads that the Third and Fourth had dropped completely and I had hoped would remain untouched.
If Nu Who wanted to pick up from the first Four, they ought to do as the First Four did. Mostly original episodes with the occasional reappearance of a previous foe. Even the Master got that treatment, being a followup of the Warlord from the War Games, given so many many appearances during Pertwee's era and only four during Baker's. The Timelords were given the same treatment, only a few appearances during Pertwee's era and Baker's tenure.
The Daleks, the Cybermen the same. Unit was expanded greatly on in Pertwee's era from Troughton's, but almost forgotten during Baker's.
So far, there has been no successor to Tom Baker. The closest used to be McCoy, now is Tennent (in his own acting, strong presence).
Si-Fy and Fantasy, that is where my heart lies. To Doctor Who and its 18 years of brilliance, still waiting on the 50 yr anniversary!