RM2 wise there were a few racial bonuses to skills, and penalties.
Elves +25 to meditation, dwarves -50 to swimming come to mind.
Those mods are signifigant, especially for the diminishing returns. . .An elf with 10 ranks of meditation has a +75 before stat or level bonus, a dwarf with 10 ranks of swimming is at +/-0. (A dwarf in that layout needs 5 ranks just to swim as poorly as an untrained human.)
IF the bonus is to reflect environment, I'd say ranks is best, as that's learning just like leveling and buying ranks. . .if it's genetic, something like "Elves meditate rather than sleep, so they have a knack for it." or "Dwarves are denser than water and their body proportions are wrong for the mechanics of swimming" then a bonus may be more appropriate.