In Fergana itself there isn’t much to do as such. But there is a bus station in the center near the market, from where you can go to Margilan to see the silk factories, to Rishtan, and to Kokand. Just keep in mind that transport stops running fairly early. Transport is very cheap, and intercity travel within the Fergana Valley is well developed.

To sum it up: in Margilan — see the silk combine, in Rishtan — the potters (an entire street of ceramics, where you can watch the painting process), in Kokand — the Khudayar Khan Palace.
As for what’s better to choose — Khiva or the Fergana Valley — that’s a very difficult question. It depends on what you’re looking for and what you love more. Khiva is medieval history and an almost untouched old city. The Fergana Valley is about the real Uzbekistan, as it is at the very core of its culture.

I’d recommend buying a 2-day tour to the Fergana Valley. Many companies run such tours in late September–early October, when the heat subsides. You’ll have a guide, and group excursions in Rishtan and Margilan are cheaper. In Fergana they also offer wine tastings at a local winery. They’ll also plan all the logistics and accommodation for you. The Margilan bazaar is mostly ordinary Chinese consumer goods. There are shops at the factories where you can buy something more interesting. Khiva is completely different. That’s history, an ancient city. Here it’s more about national color, and you’ll also taste the gifts of autumn. The tastiest fruits are in the Fergana Valley.

There is also local wine production there. As for wine, I can recommend the quince wine from “Wine Garden” — we went to the Fergana Valley, the winery is located there, and they organized a tasting for us, which almost everyone liked). You might also find it in Tashkent.

Can the silk factory, ikat and suzani workshops in Margilan, as well as the pottery workshop in Rishtan, be visited independently, or do they only run tours for organized groups?

On which days does the bazaar in Margilan take place? They say it’s more impressive than the one in Tashkent.

And a completely tactless question, but I can’t help asking it. If we suddenly can’t allocate enough days for the trip, what should we choose: the Fergana Valley or Khiva/Khorezm? I understand these are radically different places. But after Bukhara and Samarkand, won’t Khiva sort of blend together? In terms of history, a lot — if not everything — will already have been covered in the first cities. And Khiva is logistically very remote.
Please don’t scold me)