I believe the main problem lies in that the Scout has so many tools and advantages over the Assault that their few disadvantages are entirely negated and then some. Below is a general list of pros and cons for Scouts and Assaults

Scouts have to their advantage:
Lower scan profile
Better scan precision
Better passive scan range
Easy access to effective cloaking
Superior strafing
Superior flanking
Superior chasing
Superior escaping
Smaller hitbox that can often lead to false positive hits
More stamina
More stamina regen
Faster shield regen (the armor-based Amarr Scout is even superior to the Caldari Assault here)
Higher jumping height for getting over railings/certain areas of walls
Two equipment slots
Superior racial bonuses that put them head and shoulders above any class besides Sentinels and are always effective
Access to certain specialty weapons that are most effective on a Scout
No problems with handling common Assault-type weaponry
Highly effective in almost every situation

Scouts have to their disadvantage:
Lower average EHP
Slightly reliant on positioning
Uh...


Assaults have to their advantage:
Comparatively high average eHP
No problems handling common Assault-type weaponry
Serve as an effective distraction for flanking forces, but anything used right can too.

Assaults have to their disadvantage:
Can't jump over many railings, those that can be jumped are inconsistent with when they will allow you to pass, must jump perfectly
Poor scan precision, many enemies can be TACNET-invisible even undampened
Poor scan range, enemies are on top of you before they show up on TACNET if they show up at all
Poor scan profile, many enemies can pick you up on their TACNET and act accordingly
No access to effective cloaking, making it easy for unseen enemies to pick you off at range
Overall inadequate mobility for escape from even Sentinels
Overall inadequate mobility for chasing anything faster than a Commando or Sentinel
Second lowest number of equipment slots, tied with Commando
Generally inferior racial bonuses that often do little to nothing to enhance their role
A larger hitbox that often has few to no hit detection issues
No specialty weapons that can be utilized by them better than any other class (Amarr Assault + ScR excluded)
Often reliant on positioning


I may add more as I think of them.