@Mburn7 As I recall, Day’s Undoing was nerfed (cost increased from 6 to 10) and Avaricious Dragon had its ability changed (spells drawn have their cost reduced by 3) before any Red/Blue planeswalker was released. Though this applies more to the first category of cards being nerfed because they could have caused an infinite loop.
I’ll go with the cynical take that Hibernum stopped balancing cards after a while because they were given the requirement to catch up with paper MTG on set releases which pretty much sucked up all their resources.
That and the forums increasingly became hostile to the developers so it may not have seemed to be worth the effort to respond to community feedback.
As to whether auto-include cards are a bad thing for the game. I would say mostly yes. They restrict the viable deckbuilding avenues for the game, and so should be minimised to avoid the meta being defined by the same few decks.
But at the same time, I agree that true balance is a near-impossible task and may not be desirable for the business. Resources devoted to card development (as with any other aspect of a business) are limited and sometimes creating an auto-include card helps open up options in the absence of a more well-balanced card pool.
Take for example Nissa’s Pilgrimage. I would consider it an auto-include for Green decks early on in a player’s MtGPQ journey. But as you get access to and include more and more Green gem conversion spells, Nissa’s Pilgrimage’s propensity to get destroyed by Green gem conversions make it less and less appealing to have in the deck. This makes it a great card to get people started when building Green decks but there are still downsides to it.
Another factor I believe is whether the card contradicts the colour wheel or makes it less significant.
For instance, Tamiyo’s Journal granting cheap recurring draw to all colours and Corrupted Grafstone providing on-colour gem conversion to all colours. While those cards made deckbuilding in SOI and EM a no-brainer, I don’t think they were healthy for the game. They overrode the weakness of the various colours which made many decks more same-y.
Likewise, Decimator of the Provinces, Metalwork Colossus and Heart of Kiran providing big and cost-efficient creatures to the colours which don’t usually have access to those was to me another offender. Though I attribute this to the escalating power creep that Hibernum attempted in order to keep players interested in (and hence also interested in spending on) MtGPQ.
Cards that to me (though I must say that I never really played paper MTG and hence could be wrong about this) contradict the colour wheel are River’s Rebuke, Startled Awake and Storm the Vault / Vault of Catlacan. Though the ones in Ixalan seem to follow closely to their paper versions so maybe I’m just really out of touch.
So I think we should try not too have too many auto-include cards in the game lest they start constricting the meta too much. But a few here and there, especially if they aren’t Colourless, would be acceptable and as mentioned above perhaps even beneficial.