Both test can be good for determining the strength of the concrete.
When using cylinder, you need to use a formula to convert the achieved result into those of equivalent to cubes.
When using the cubes your strength determination is Load at failure divided by surface area of the cubes.
Use of cube or cylinder is dependent of the standards which you follows at your country. Above stated statements are for Indian Standards.
Design parameters for structure might change as per the standard methods of determining concrete strength (as i have not used cylinders for concrete, i do not have much idea about it but reading through ASTM standards will give you deep insight of it).