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Nothing prevents a miner from omitting transactions from their own block template. They will just make less money in fees compared to other miners that do fill up the block to 4000000 weight units according to the current consensus rules.
At a pool aggregate, you're correct. At an individual miner level, if you don't want to mine something, then you don't mine something - yes you may leave sats on the table, but under a global consensus you may simply be forced to do that.
So although I am in the "yes it was suboptimal, in hindsight" camp, it's more important to not meddle and have stability than to change it every time we perceive something to be suboptimal, unless something is truly at stake. If we change incentives with the direction of the wind, Bitcoin development becomes like the Fed, and Bitcoin becomes like Ethereum.
Long-term stability is Bitcoin's greatest asset, even if that means that there will be periods where we have spammers or other unwanted hype. Those often die off automagically.
What prevents a miner to unilaterally implement, today: I from here on price per byte including witness (no discount) and my block templates will from now on be 1MB including witness data?