I think design wise it's generally assumed you're taking more than one school. Warblades and Crusaders only learn two 9th level maneuvers. Only Swordsages get more, but they're designed to be used with multiple schools. Also, it was a common wish that being able to rebuild the current schools using this system would be retained, and they all have more than 3 maneuvers per level at lower levels.
It's true that current ToB classes are designed to make use of multiple schools, but the proportion of maneuvers that an initiator can know from a given school (within the window that said maneuvers are optimal to learn) is twice as large for 9th level maneuvers.
For example, a crusader learns 1 8th-level maneuver and retrains one maneuver to 8th so he has 2/3 of the total maneuvers available to him. But he gains 2 9th-level maneuvers and retrains 2 maneuvers to 9th, so he has 4/2 of the total maneuvers available to him. I'm only using a single discipline's ideal # of maneuvers known because multiplication is hard, but what this demonstrates is that initiating classes will have twice as many opportunities available to them to pick up 9th-level maneuvers, so it makes sense to me that there be
more 9th-level maneuvers instead of
less.
The large number of low-level maneuvers makes sense. I forgot classes granted so many at level 1.