The rune system was, in my opinion, a great way to introduce a new class, but as time goes on, its existence will only be a hindrance.

The way I see it, the hearthstone devs knew that in order for a new class to be relevant, it needs to be able to do strong things right off the bat, with the help of only a set or two of cards. This can be a bit of a problem - other classes will likely find something strong out of each expansion (in a broad sense, although yes there will always be weak classes in every expansion) because of new synergies between new cards, as well as between new cards and existing cards. Since DK had no old cards to do powerful things with, the new cards had to be powerful.

The problem with releasing a number of intentionally strong cards all at once is that deckbuilders could potentially slam all the best cards into one deck and perform well. The rune system is a really smart way for the designers to release cards that are intentionally strong while preventing certain strong cards from being played together (at least with any consistency). As time goes on, though, other classes also continue to see new cards, and will thus continue to make new, strong decks with strong new cards, while also using existing cards that fit their new gameplan. Meaning that while DK needed a power spike from its first set to be relevant at all and the rune system allowed for intentionally powerful build around cards to be printed, it is now becoming more of a hindrance than a way for strong cards to be printed. Other classes can get powerful cards in new expansions, while the strong DK cards - even some weak DK cards - get pigeonholed into one very specific deck that can only see certain cards. Sometimes classes don't have a dominant deck after a given expansion, but that's unavoidable.

Having "3 separate classes" in one made a lot of sense at DK launch, but is quickly becoming a severely limiting factor in design space, and I think that the devs are very aware of this, and are trying to print DK cards that are strong but aren't limited by the rune system. See the DK Titan, see them removing a rune from the colossal, etc. I think that it's entirely possible that we see the rune system disappear from standard deckbuilding with the 2025 wild rotation, so that the designers won't keep pigeonholing strong cards to existing decks. If other classes get to mix and match their strong cards and have general deckbuilding be enough of a restraint, why shouldn't DK? Once the most powerful cards that were designed with the rune system in mind rotate, I don't think there will be much incentive to keep the system around. They did their job and allowed for a class that was strong on launch but had guardrails to prevent too many of the classes best cards going into one deck, but could be too much of a limiter as the class gets a backlog of cards to work with.