Basically, their choices are keeping Cyrillic, and therefore implicitly culturally aligning themselves with Russia (or, to phrase it in a different way, exposing themselves to Russian cultural dominance); or switching to Latin, and implicitly culturally aligning themselves with Turkey.
It's not a question with a single definitive good answer. Different ex-Soviet republics tackled it in different ways. The article points out that Azerbaijan and Uzbekistan switched, for example, but e.g. Kyrgyzstan did not.
The other problem with every switch (including the previous ones) is that it affects all existing written materials, especially books and textbooks. When Soviets originally switched most Central Asian republics from Arabic to Latin back in 1920s, they used it to great effect to control what kind of materials the new generations would have access to, very similar to what Ataturk did in Turkey. Same thing applies today: switching the alphabet allows the new governments of these countries to define the majority of the written corpus that their citizens will have ready access to.