MS is maybe the most important on its own, throughout all stages of the game and especially during the laning phase, where there are strict tactics you can follow to get leads, and a lot of them depend on having correct positioning, poking and avoiding damage. All of these are directly affected by how fast you can move, and that extra early MS is VITAL to that success.
Also, it offers a small boost to your AP or AD, but sometimes it can make a difference. As soon as you spend 300 gold on boots, or around 1k gold for tier two boots, you get an even larger amount. Seeing how boots are a core item for every champion (Cassio no boots lul), you will always have some bonus stats. A lot of champions also have abilities that increase their MS, thus their AP or AD, and some of them also build more items that grant them MS, like Triforce, Dead Man's Plate, Lich Bane etc.
So, the point is that, apart from the bonus MS at the start which is crucial, you also get some offensive stats passively and during all stages of the game.
Transcedence is rarely picked because it's a rune that grants you 10% CDR at level 10, and also grants AD / AP if you exceed the 40% CDR cap. It's almost safe to say that you need quite a lot of items to reach that cap, making it so that this rune is basically useless until after you hit level 10. Even then, the first reward is just 10% CDR, which isn't really that much. The gold value of 10% CDR is just 247 gold,, which is basically useless at that point. Also, taking advantage of the cap thing is also hard and require you to have at least 3 items to gain minimal some stats out of it.
The game is so early game dependent now, that you want to have as much early power as you can from early on. Having to play essentially half the game with one less rune runs the risk of getting ran over, especially in higher elo where people will take advantage and abuse that.
Taking Transcendence is only a niche pick for certain champions that 1) want to have 40% CDR and 2) their itemization doesn't allow for it to happen.
An example could be someone like Malzahar. The fact that he needs Rylai's, Liandry's, and Morello means that his other options usually only get him up to 30% CDR. Having 40% CDR is really good on him though, since it means that he can use R more often, which is important, so sometimes, Malzahars can take that rune. I won't be surprised though if, even then, they still picked Celerity.