The best replacement for alleles is genes.

The best alternatives to alleles are rated as following:
★★★★★  genes
★  traits
★  recessive alleles
★  locus
★  polygenic traits
★  multiple genes
★  polygenic
★  loci
★  chromosomes
  polygenic inheritance
  incomplete dominance
  heterozygous alleles
  two recessive alleles
  gametes

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Speaking about alleles, one probably shouldn't forget about incomplete dominance.

Other search terms related to alleles and their ratings are:
★★★★★ incomplete dominance
★ multiple genes
★ codominance
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