I want to spend some time in Uzbekistan and then travel to one of the other Stans for a jeep safari to see some great mountain scenery (not Pakistan though because I've travelled extensively there). If you had a week or perhaps a bit longer which country would you choose? Kyrgyzstan sounds great but I'd love to hear your views.

Kyrgyzstan, Tajikistan, and eastern Kazakhstan all have magnificent mountain scenery. It depends on what you are looking for. Also, it depends in part on what time of year you're planning to go.
For my part, I prefer Kyrgyzstan, because of its well-developed system of homestays and because I prefer greener mountains and tinier villages or jailoos (mountain pasture seasonal settlements). Still, I wouldn't have wanted to miss any of them.
Kazakhstan has wider highways and more developed cities along the way. If you go to the Altai Mountains, however, you will be in the region from which surged, in turn, the Huns, the Turks, and the Mongols, as well as, many millennia earlier, the American Indians. It gives one pause to wonder what in this area nurtured that. You may still need permission to visit the Altai Mtns, though I've heard rumors that may be changing.
Tajikistan's is of a more austere type of beauty, with the mountains more rocky. Tajikistan has the advantage of the greatest remoteness, in the High Pamirs of legend. But although everything else there costs less, jeep transport is extremely pricey, and there's essentially no alternative.