"From God, to Kane, to Seth, I am his right hand man" ~ Seth, Brotherhood of Nod, Command & Conquer, 1995
(People always give C&C:RA too much credit IMO, the original C&C was overlooked. But then I imagine Dune 2 players saying the same about C&C!)
In Dune 2 you could wall-in your repair center (or build other buildings around it); if you did so transport aircraft would come and get damaged vehicles from the battlefield, bring them to repair center and bring them back. Too bad I never found anything like that in any other relevant RTS since then.
There were some attempts to make RA1 an actual prequel in the C&C timeline but its success resulted in the timelines diverging too much.
I actually also kinda liked C&C Generals despite it having no relation to C&C other than the branding but sadly that series was pretty much doomed from the start.
The original C&C was released as "Command & Conquer Teil 1: Der Tiberiumkonflikt" ("tiberium conflict", instead of "tiberian dawn")
The original RA was released as "Command & Conquer Teil 2: Alarmstufe Rot" ("code red", instead of "red alert")
C&C2 was then released as "Command & Conquer Teil 3: Operation Tiberian Sun" (instead of simply "tiberian sun")
By the time C&C2 had been released the Internet was becoming a thing and still predominantly English so the different numbering schemes began causing trouble for English-speaking Germans.
I think they gave up on consistent numbering by the time RA2 came out (it wasn't actually called "Teil 4" IIRC) and if I recall correctly they just stuck to the English numbers with C&C3 onwards (yes, that means technically "C&C3" was ambiguous in Germany at that point).
<spoilers> In Red Alert there are some clues that the setting is tied to that of the original Command & Conquer however. For example Kane shows up on the Soviet side and it's strongly hinted that he is the same Kane as in Tiberian Dawn. This led to some fan theories that Kane is immortal because he's literally the Biblical character Cain, which was pretty plausible if you consider the other Biblical references ("the land of Nod" is where Cain was exiled and Kane is the leader of the Nod Brotherhood; Seth is Kane's second in command and also the name of Cain's and Abel's brother). I think there were also some conspiracies based on the re-use of German voice actors (I think Einstein's assistant was voiced by the voice actor who also voiced Kane? I don't think this is the case in the English version). </spoilers>
Ultimately this probably has more to do with budget constraints and that Biblical imagery is a cheap way to introduce some drama and I'm not sure whether this was ever intended as more than a not-so-subtle nod (heh) to Tiberian Dawn.
Fun fact: one major criticism of Tiberian Sun was that the publisher cast a new voice actor for Kane who sounded nothing like the first one fans had grown to love (his voice was also much lighter, leading many to joke that he sounded a bit emasculated). IIRC the official explanation was that the original voice actor had demanded too much money. In addition to the disproportionate hype the game had received prior to release that was also often pointed out as one of the major reasons it wasn't as successful as anticipated.
Took too long and didn't bring much new stuff.
RA came shortly after TD. Not much had happend with strategy games till then and they just used the same engine and took everything for TD to the extreme (story, weapons etc.)
One year befor TS we got Starcraft, which took strategy games to another level, so they HAD to do more, but they didn't.
Anyway, the hype was probably enough to make enough money for the other titles, haha.
Whether TD and TD Gold were actually different engines I don't know but it must have been at least an improved version of the same engine.
I think you're right that SC doomed TS to fail. SC was lauded for having three factions that are actually fundamentally different to a much greater degree than had been done before (e.g. Dune 2000) and had great storytelling compared to the well-done but low-budget and often cheesy narration in TD and RA.
TS tried to one-up the genre with its cinematic cutscenes but they ended up creating an actual protagonist so the result felt much more like watching a movie than something you're actually involved in (especially when the protagonist does more than reacting and following orders -- which was the sole reason having a protagonist became necessary at all).
Also, the engine was different and they tried to cash in on technological superiority with big talk of "voxels" but the end result just looked fuzzy and often sterile. They also tried to do the "multi-faction" thing by introducing the mutants (though not as a playable race) which confused the setting even more. TD was about futuristic modern warfare, TS was 100% sci-fi. In that sense I guess Generals was a bit of a return to the roots.
I played C&C through 3, but really hated the 4th. They ruined it by trying to make it some half-baked MOBA type thing. I still haven't even finished it.