My suggestion regarding this is a 3-tier grading system:
The first is to lock in the AM and PRO champions so that they're both competing in PRO (you do this already).
The second is to assign each driver a point value based on where they finished in the previous season's championship. You'd give max points for the top driver in each class and decrease it as the positions go down. This rewards drivers that are loyal to the series by signing up for consecutive seasons.
The third is the normal driver grading system, but to award a second set of points based on laptime.
You then add up the point totals, with the top half being in PRO and the bottom half in AM.
The benefit of this system is that a driver's overall performance (and implied skill) is measured, as opposed to their one-lap pace on a specific car and specific circuit. A driver may simply be a bad qualifier, but a good racer that always finishes ahead of where he starts, which is something the current system does not take into consideration.
To give a practical example, here is what a hypothetical Season 4 lineup would look like if we take the current season's championship positions and assume that everybody got the same laptimes they did in the initial grading:
Some notes on this:
@TNR_KING_FILO,
@TeamEdge702 and
@Mikey24 all had weak gradings but a strong season, and as such would be graded higher than a pure lap-based system.
@Glenalz81 and
@TORCHON had good gradings but either didn't compete or dropped out early, which meant that they took up potential car allocations from other drivers and were over-rewarded for what was simply a 5 lap run on a single night.
I believe this new system is fairer for all involved and I recommend you consider it for the upcoming season or any where you do driver grading and car allocation.