UNSC Marines are not clones. Cloning of a full person eventually leads to metabolic cascade failure, a degenerative and lethal disease, making clones ill-suited to combat. The sheer expense of having to grow and train these clones, rather than recruit from the readily available populace, is also a factor against it.
Halo 1, 2 and 3 uses certain character models common to individuals that must be different people because it would be too much effort to create unique models for every Marine in the game. Most Elites and Brutes, and other Covenant characters, share character models, with minor differences in character. There is actually a lot more variation among Marines than the Covenant.