The top alliances have not had any issues with war matching from the beginning. Regardless of whether matching was done by alliance scores or hero comparison, the algorithm quite reasonably pairs up these full, active, hero-heavy alliances against each other. So your suggestion that all the recent changes were in some way aimed to help the top alliances is off-base. We are uninterested in a walk-over war. We are competitive and want to show we can beat the best, or at least go down trying.
There have been several changes to the war matching. The CTO has been responding over in this thread recently, so it might be worth reading there.