Which islands in Scotland would you focus on?

I would maybe pair Skye and Lewis but skip the northern isles or drop Skye and vist the northern isles
Lewis is a stunningly stark landscape and Tarbet to Stornoway might be my favourite journey in the UK after visting last year

The natural partners are Skye with Lewis and Harris OR the Northern Isles of Orkney and Shetland. Choose one or the other and use the days 'saved' to give more time.

Skye, Lewis and Harris are mainly about scenery and there is some stunning walking. The Northern Isles have the prehistoric remains, especially Orkney. Scenery is good but not quite on the dramatic scale of Skye or Harris. Walk Highlands is the walkers Bible so check out walks on that. There is plenty of choice from short easy walks to the real head bangers stuff.

You are more likely to see puffins on Shetland - Sumburgh Head is the classic spot and you can get within a short distance of them. For Skye, Lewis or Harris you would need to do a boat trip. I've seen otters, wales and dolphins regularly on holidays to Shetland.

I agree with Richard and Wasleys about doing one or the other. And when you say 2-3 days do you mean 3-4 nights which give you 2 or 3 full days? Or 2 nights which just gives you 1 full day for touring.

To me the difficult thing about Orkney and Shetland is that the transport to/between/back can be a bit difficult with weather delays and equipment breakdowns. I would allow some days before and after on the Scottish mainland to give yourself some flex time around your long-distance flights.

I went to Orkney and Shetland in August 2023. I am going back to both in July 2025 I was so blown away by them. The puffins had left already in August but you'll have good spotting in June. There are several FB pages I follow for both areas and they do have puffin reports.

There is a new guidebook out for Shetland written by 2 local women who both have a presence on FB. Here is the link to one with the guidebook.

https://shetlandwithlaurie.com/?fbclid=IwY2xjawGwdcRleHRuA2FlbQIxMAABHanlGbVAuiTBC4HFlGBx3iFeGqO6LRt39JrNvpRZfvtnwfEBDfdwLpUE9g_aem_cBCO7mvnGR-h1WBe_fWxzA

If you are at all interested in seabirds, I did a boat trip with Shetland Seabird Tours. The captain and owner of the boat, Phil, was impressive. At one point he spotted a pod of Risso's Dolphins. He stopped the boat, whipped out his camera with a long lens and said he was helping to document which individuals were being seen in the area for conservation purposes.

https://www.shetlandseabirdtours.com/the-team/

For seeing Puffins on Orkney try the Broch of Birsay (a tidal island which can only be accessed on either side of low tides so requires careful planning) and also around the Kitchener Memorial. Both are fairly near each other and also near Skara Brae and the Cliffs of Yesnaby.

For outstanding scenery and coast, I'd also choose Skye , with Harris/Lewis - which also gives you the chance to pop over to Berneray and North Uist potentially also which are very different again.

Shetland is more rugged and scenic than Orkney which is largely flattish farmland though with some fine coastal cliffs (though not on a par with those on Skye or Mangersta on Lewis.)

Harris is outstandingly beautiful and given your comment about wanting to enjoy natural beauty, those islands I've listed have it in spades and yet are all very different. Your issue, especially on Harris , may be in finding the accommodation you want at this stage.

It doesn't work with the day tour from Oban but from Mull, you can do the add on boat trip to the Treshnish Isles which is outstanding for puffins - they are virtually around your feet.

Shetland's Sumburgh Head is very good too, though not with anything like the same numbers but of course, you can easily see them from the roadside. Delightful!

There are some excellent boat trips from Skye - from Elgol and Portree itself - which have a good chance of dolphins and various whales; Minke mostly commonly but also humpbacks sometimes feed in the Sound of Raasay. Occasionally Orca but they are perhaps more likely between north Mull and the Small Isles.Always keep a lookout too when on the various ferry crossings!
The family last year going over to Staffa had the joy of a school of dolphins swimming near the boat.

Sea eagles are fairly common too.

Skye, Harris, Lewis and Berneray/N.Uist offer world class walking and certainly some of the finest virtually deserted white sand beaches you will see anywhere.Glorious.

The great thing about all the islands is that they tend to be breezy so midges can be less of an issue as a smidgin of breeze keeps them away.A still, calm evening however and out they will come though keeping on the move simply by walking tends to leave them behind.