A lot of fans like the idea of revisiting things or characters they found particularly exciting. They can have this notion that if we revisit those things it will be exciting again. But context is everything. Part or the original excitement was the novelty which you no longer have in a revisit. So revisiting a favoured character will only be interesting if there is something genuinely fresh to bring to the game and it's justified by the larger story. Otherwise it's just meaningless pandering.
TNG began the era of connect-the-dots that continued through the following series. And connect-the-dots is something that's been going on in Trek lit since the beginning. But candidly it's rare that this practice really works and it's usually just more pandering. It also makes the fictional universe seem that much smaller every time it's done. It isn't necessary for everyone to know everyone else and for everyone to be privy to everyone else's experiences.
Please, let's keep it to a minmum.
Truthfully as much as I like Star Trek Continues and the character Elise McKennah I am somewhat disappointed seeing the idea of her character in the TOS era. It's so obviously a connect-the-dots to the TNG era in the face of no evidence that ships' counselors existed in the TOS-TMP-TWOK era. We also don't see evidence of it in the Enterprise C era (although they could have been there). There's supposed to be about a century between the TOS and TNG eras so why the insistence to introduce a Counselor now? It's simply a connect-the-dots move.
The idea of the proto-holodeck is more iffy because GR did have the idea back in the day and it did appear in TAS. But for a lot of folks not knowing those things it is a connect-the-dots move. I don't really mind it, but they could have done without it.
What's being done in Phase II is also a connect-the-dots move and one (in my opinion) which doesn't make sense in the "real" world of TOS. Why would Starfleet drastically refit a ship only three years into its five-year voyage and then refit it again (even more drastically) a few years later just prior to TMP? That strikes me as a lot of unnecessary effort and downtime. But the Phase II folks feel compelled to cement this connection between TOS and TMP to rationalize the visual differences between TOS and TMP. It's an indulgence that in the larger scheme of things---telling compelling stories---doesn't accomplish anything. It's just "because."
TAS did it with Robert April. In a more real world perspective it isn't necessary for Kirk and crew to have ever even met Robert April. Certainly the story he appeared in could have easily been told without him. But the writers wanted to indulge in connect-the-dots. It didn't add anything to the story even as it didn't really take away anything from it either. It's a touch of fanwank and in that instance it did no harm. But I certainly wouldn't want to see this all the time.
Of course, that's just my opinion.
While not a massive 'refit' military aircraft and ships are upgraded all the time, as are commercial aircraft. This would be difficult to do in small bits and pieces with a ship traveling for years many lightyears from home, so perhaps doing all the upgrades every few years would make sense. How much is this done today? It's the main reason that military contracts are all cost-plus. Often the military changes what it wants several times while the aircraft/ship/hoodiggie is being developed and built. Specs change many times often before the first craft is built. When a bomber that was used in Viet Nam is being flow today, it has modern computer guidance installed, it's not running on the system it used in 1964. However, it often looks much the same from the outside. (I am a military-industrial complex brat. My father spent most of his life designing and upgrading military equipment, including, the last thing he did... the first system that shot down incoming missiles, which was done for the Navy. Reagan based his idea for 'Star Wars' on that system.)
Concerning the ship's counselor, I suspect this has much to do with the actress being Vic's wife. Also, TOS has a very sexist feel that I suspect many people today aren't comfortable with. (I was not comfortable with it as a 'tween.' at that time.) That is not Roddenbury's fault, he wanted a female No. 1, but there was a lack of vision in the suits, and its one of the things that dates TOS to the 1960s. The introduction of this character allows the production to counter that problem without entirely reworking the rest of the characters. They are also giving Scotty a bigger role than in TOS.
Background recurring characters work for some things and not for others. It would have made sense that Kirk would have been reporting to a particular admiral, rather than hearing from a different one with each order. Would it be wrong for fan films to correct this?
I don't know that I had any desire to see what happened to Apollo, but I liked the story. The Orion Slave Girls did seem to beg for some updated twist. That is clearly our ideas intruding on those of the 1960s. It was a revisit, but it took something that was just a passing matter in the background and made it into a central story.
Most dramas today have a story or two each year on the supporting cast. Usually, Castle focuses on Richard Castle and Dect. Beckett, but we get shows that focus on the other police officers once or twice a year. Those types of shows did not exist in TOS. I don't think the greater use of the character of Scotty in STC is wrong or out of place, it's probably a more realistic take on how the crew would work. There was no Chekov show, no Sulu show. Filling those in is also a modern update, but its one I have enjoyed from Phase II.
Part of this I suspect is just how much you like fan efforts. I happen to enjoy them a lot.