A lack of lower-CR legendaries in the 2025 Monster Manual makes it hard to have a big boss fight from levels 1 to ~6 (which, I would wager, is where the great bulk of 5e groups play)

The lowest-CR legendary in the 2025 book is the unicorn, a Celestial. It is narratively very niche as a boss encounter, and Unicorn's Blessing suggests that it is supposed to support allies in combat. It would take considerable reflavoring and modification to turn a unicorn into something more appropriate for a low-level villain.

The second-lowest-CR legendary in the 2025 book is the aboleth at CR 10, a big jump from CR 5.

Trying to field a non-legendary as a big boss runs the risk of it getting hard-controlled into uselessness by Command (which, in 2024, bypasses virtually all Immunities and does not even require the target to understand it), Suggestion (which does not require the suggestion to be reasonable), Blindness/Deafness (which can be hard to break out of if the victim lacks Constitution saving throw proficiency), and other spells. For example, as per the 2024 encounter-building table, a single CR 5 enemy would theoretically be beyond the capacities of four level 3 PCs, but the 2025 book has many CR 5s who would crumble to a single Suggestion.

Minions as backup can do only so much, especially if they cannot reliably break a spellcaster's Concentration.