For the most part, I love the Legion rules as streamlined, yet strategically interesting.
However, the one part of the rulebook that most often has me feeling like there was a missed opportunity is Height and Vertical movement. In my opinion, there should be an advantage to taking high ground, given that objective play provides a strong disadvantage to spending time getting into and out of an elevated position (unless you put a supply token there for RtS objective). As a result, there is a disadvantage to creating and using tall terrain with climbing surfaces.
Climb/Clamber - this was an opportunity to make grappling hooks useful, to make climbing vehicles more useful, and to make action economy more intriguing. I do love the risk element of climb (more actions, but safe) versus clamber (risk of death), but the rules that require unit leader base contact AND THEN finishing the climb/clamber at the edge of the higher position means you're burning four actions to safely get from a position on the ground to a position you want at the higher height (one move to get into base contact, two moves to climb up to height 1, and one move to move away from the edge). While many people get around this by using stairs/ladders/elevators to grant free vertical movement, I think that goes too far the other direction and makes climbing a useless rule. Stairs/ladders/elevators also seem lightly supported by firm rules--I'm for granting flexibility to players, but there is a lot of room for fudging considering that the rules go out of their way to detail how restrictive the actual climb/clamber rules that must be adhered to are.
Proposed solution: I think ladders/stairs/elevators should be handled as regular move actions similar to the RAW climbing procedure--if your unit leader is in base contact with them at the beginning of the move, he can move to the other end of that conveyance with a single move action (or two moves if higher than height 1)--and end that action at the upper end of that conveyance. If you're climbing/clambering, you should be able to start your move on the ground not adjacent to the building, and move up to the building and then climb/clamber to the edge (or vice versa and start in contact with the building and move according to your template at the top). If you have grappling hooks, you should be able to treat anything under Height 2 as reducing your speed by 1 (the reduced speed simulating the time to use the hooks, and not considered 'difficult terrain' to avoid stacking with environmental gear).
Attacking with height advantage - This is another one that many people find counterintuitive. There is no inherent advantage to attacking from above. There are the ancillary advantages of having a slightly better chance of ignoring cover based on your LoS, and avoiding melee on the ground (though Luke can Jump and Vader saber-throws). In exchange you have to spend multiple actions to get up (away from most objectives), and heaven forbid you need to get them back down again.
Proposed solution: I don't necessarily think there should be an attack bonus, but perhaps automatic light cover up to Height 1 and maybe even heavy cover beyond Height 1 granted to the attackers.
Summary: I think the game should encourage 3D play as much as possible. Height-varied combat makes for a more interesting game and a more visually appealing and dynamic board. I don't think these changes would negatively impact game balance because the game rightly remains objective-based. Making the climb/clamber rules less onerous provides a new strategic option that players must balance as a part of action and turn economy.