The sequence is not arbitrary and it is not alphabetical — it's a build, and it's also a route, and those two things happen to align, which is why this itinerary works better than most people's first instinct.
Athens goes first because you need the context before the spectacle. Three days in Athens — the Acropolis Museum, Plaka at night, the National Archaeological Museum if you have the stamina — gives you the historical frame that makes the islands mean more, not less. It also absorbs your jet lag and any flight delays before you're dependent on ferry timing. Front-loading Athens is non-negotiable: do it at the end of the trip and you'll be too tired, too sunburned, and too eager to get to the airport to give the city its due.
Santorini comes second, immediately after Athens, because it's the emotional peak and peaks shouldn't sit in the middle of a trip getting buried by everything after them. Two nights, not four — this is a deliberate rationing. Santorini's crowds and prices punish overstaying, and the caldera view doesn't improve on day three the way a Naxos village meal improves with a second or third evening. You get the postcard, you get Oia at sunset once, and you move on while it's still vivid rather than souring from overexposure.
Naxos is third because after Santorini's intensity, you need the island that lets you actually relax and eat well without a crowd of cruise-ship day-trippers at every taverna. This is the substance stop — the one that proves Greece isn't just caldera views, it's also a grandmother's kitchen in Halki and a near-empty beach at Plaka. It's positioned in the middle of the trip deliberately, as the longest, least rushed stretch, because by day five or six you've earned unhurried.
Paros comes last not because it's the weakest link but because it's the exit ramp — close enough to Athens's airport ferry and flight connections to make the final return simple, with just enough of its own character (Naoussa's harbor, Lefkes up in the hills) to make the last 36 hours feel like a destination rather than a layover. Ending on Paros rather than Naxos or Santorini is a logistics call disguised as a soft landing.