The best replacement for illumina is affymetrix.

The best alternatives to illumina are rated as following:
★★★★★  affymetrix
★★★★  454
★★★  solid
★★  ragnarok
★★  agx
★★  koni yellow
★  kyb agx
★  sanger sequencing
★  sequenom
★  koleston
★  roche
  ion torrent
  koni yellows
  d-spec
  ion proton
  tokico blue
  affy
  454 sequencing
  abi
  life technologies

Your alternative for illumina is not listed? Suggest!
Speaking about illumina, one probably shouldn't forget about ground control.

Other search terms related to illumina and their ratings are:
★★★★★ ground control
You have in mind a companion for illumina and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of illumina in all years. Click on graph for more.
illumina
affymetrix
454