Gene expression is often tied to the environment the organism is in. Mere possession a gene isn't enough to benefit from it. Some expressions don't take effect immediately, but rather activate in subsequent generations.
Epigenetics is a whole equally large layer on top of this system. A single-focus approach may not be sufficient, and even if it is, it's not likely to cope with environmental entropy very well.
 I understand gene to mean some ill-defined, not necessarily contiguous set of genetic sequences (DNA, RNA, and analogs) with an identifiable, particularized expression that effects reproductive (specifically, replicative) success. I think over time "gene" has been redefined and narrowed in a way to make it easier to claim to have made supposedly model-breaking discoveries.
 Some others on HN have made strong cases for why epigenetics isn't a meaningful departure from the classic genetic model; just a cautionary tail for eager reductivists who would draw unsupported conclusions from the classic model. See, also, note #1.