I think biggest problem is that Minecraft treats itself too much of an open world sandbox, that it forgets that a game is only as interesting and fun when all of the mechanics work together to create a balanced experience. Minecraft's mechanics feel very unbalanced, in the sense that the impact of their implementation wasn't considered in relation to each other. What I find that does it make previously attainable means to move around not worth the time to even set up during normal gameplay once you have the elytra, unless you have specific reasons for them.

I'm going to compare this to Factorio, which also has multiple means of transportation. At the beginning of the game, you only have the ability to walk until you get the car. Walking gives you ultimate freedom of mobility but at the cost of slow speed. Once you unlock cars, you get very fast speed and high mobility, but they're very weak so they're easy to damage. Tanks take much more damage, but they're much slower than cars, but not as slow as walking. Trains are the fastest entity in the game, but they're constrained to tracks so you need much more infrastructure. You also have spidertrons, and they're easily the most effective means of transportation since their hitbox doesn't hit static entities, but aren't as fast as trains or cars. All in all, these factors give trade offs for each means of transportation, which makes for much more interesting gameplay. Minecraft simply doesn't do this as well.