Like Loria said, it makes sense that if you choose a race that is geared in a certain direction, and then choose a class that is geared in the same direction, you should get a slightly better end result than if you choose different directions.
It's like in RL, you are born with certain talents. For instance you could be talented at athletics, ball games, music, mathematics, playing chess etc. If you are not born with those talents you can still LEARN to do those things and even train them up to a certain level.
But a kid who isn't born with a talent for handling balls, will never be as good at football or tennis as the one that has the talent.
The same things goes for the kid who wants to play the violin without being musical. He can learn the technique, what grips to use, and how to handle the bow, but the music he produces woll probably sound pretty awful.
Both of them would be a lot more successful if they chose a path that is consistant with their natural abilities.
I think it would be a lot more interesting if the races worked like that. Some races could have a particular ability for brute force, others at evasion or running fast, others at moving without being seen, yet others at different kinds of magic. The differences shouldn't be too big, but they should exist. And they should of course be balanced, so that if a race is good at one thing, it should be bad at something else.
And when they start training, i.e. choosing class, they should have a small +bonus at the thing they are good at and a negative bonus at their weakness.
Then it becomes a part of the challenge for a player who wants to advance as quickly as possible, or create the "maximum char", to choose a combo between race and class that works well together.
Personally I would prefer races to be different - but of course balanced.
If it is too hard for you to balance them, then by all means make them cosmetic.