Perhaps you should look at it this way: Alertness is a skill, whether you may have a particular knack for it or simply have been forced to rely on your senses a lot, it is an acquired 'ability'. Social skills are like this too: some people are just naturally apt at communicating with others, in whatever way, but you can learn to do this as well. Perhaps you are a psychologist and you take a trained, intellectual approach to social interaction.
If you have eyes that are far better than anyone else's, it is either an aspect, a stunt or a power.
An aspect can be used by you or against you. In the case of Keen Senses you could use it to get +2 to you roll, claiming you saw the movement and instinctively reacted to the attack. If you have Eagle Eyes, but you rely on your high Athletics to dodge, the GM might compel the aspect and say that while you might dodge, your sensitive eyes would still be affected. If you pay it off, you manage to cover or close them in time, if you take the FP, you just weren't fast enough.
If it is a stunt, your bonus is probably limited to circumstance, such as barely-lit rooms or something similar, so I feel it has less chance of being used against you. A power, however, could easily be used against you: imagine being able to see infra-red or thermal, a flashbang would be hell on your eyes, especially if you can't 'shut your power off'.