I'd scrap them and move to a "modular" system like Universities where pupils earn and bank modules/marks throughout secondary school. Allocate marks to each module which count towards some kind of "school leaving" certificate, the marks per module being based on the level of difficulty etc.
Pupils can move up to more difficult/advanced modules within each subject only when they've passed the earlier/easier modules. Some modules will be compulsory, such as basic life-skills literacy, numeracy, personal finance, personal health/safety, etc., but pupils can retake the module multiple times until they pass.
It allow pupils to move "up" through secondary school at their own pace and to their own ability. Ultimately, the strugglers should at least attain a "core competence pass" just by eventually passing most of the basic/simpler modules, even if it takes them several years, so at least leave school with some kind of "school leaving" certificate confirming basic life skill competences. Higher achievers can whizz through to the hardest/advanced modules to get to the highest level of school leaving certificate.
An added benefit is that it stops the "year by year" ethos and will put pupils of similar ability together in module groups rather than based on year groups, so struggling pupils can be "held back" effectively to take modules with younger pupils, and thus reduce the negative impact of being pushed through into more advanced/harder year groups despite not having grasped the basics in earlier years.