Autechre have created a unique and particular sonic universe, so it’s hard to say what’s best or most representative of their music, and you’ll probably get as many different answers as people you ask. so perhaps a suggested heuristic path…
find elseq (in parts 1,2,3,4,,5 (it’s the most recent and compresses much of their work strangely). chronologically, listen to Eggshell, if you like it get Incunabula. listen to Montreal or Foil if you like them get Amber. listen to Rsdio. just listen to it (and get tri repetae) C/Pach is probably most indicative of where they go next, which is Chiastic Slide. listen to Nuane. listen to Arch Carrier or Corc from LP5. Confield is quite broad, try Uviol or Lentic Catachresis or Parhelic Triangle. from Draft 7.30 listen to Xylin Room or Surripere or IV VV IV VV VIII or Theme Of Sudden Roundabout. from Untilted listen to Sublimit or Augmatic Disport. from Quaristice try IO (mons) or Tankraken. Treale or d-sho qub from Oversteps. from Exai listen to irlite (get 0) or just the whole album. their live material is worth listening to as individual pieces.
(note this just covers their albums, so doesn’t include the various EPs. you can think of the EPs from each period as similar, yet distinct. if you find any particular album interesting chances are you’ll like the other material from around the same period)
(i left out the bit where you open a small door and find a Gescom)