Many people use custom hotkeys to assign patterns. That being said, I observed some undesired game behaviors that ruin the skill control panel:
(1) Shadowraze skill: there are 3 buttons for this skill and every time a new active skill is leveled for the first time it changes position. Not only this skill, but any multiple button skill will work like this. Also, active/deactive skills eventually change their positions;
(2) Aghanim's Scepter: after completing the recipe, the ultimates may change positions;
(3) Level 25: after max stats, the skills will again have their buttons changed.
It is not impossible to play with these events happening, but it would be better if they did not happened. I suggest:
(1) fixed positions for multiple buttons skills. So if I pick Shadowraze, no matter which position I picked this skill in the pick phase, it will be placed in the bottom left in sequence.
(2) prevent the "+" button from disapearing, so when the stats are maxed the buttons won't be messed up.
About the Aghanim's scepter, I think it is more about fixing than suggesting.