I hesitated in posting an answer here as there are already very good answers that put forward a multitude of reasons which seem to fully cover and exhaust the subject. But to the question whether there is one decisive reason for the non-unification of the two Romanian-speaking states, I think the answer is yes.
(But I do not want to dismiss different other reasons, and I think they are all important.
Also, other such secondary but important reasons, pertaining to the larger European context, can be still found, like, for example, that, excepting the German unification, as a sort of counterpoint to EU integration, separatism seems to be a very important trend of European geopolitics. People usually think about German unification of 1990 as an example, but that was followed by the separation of Yugoslavia and Czechoslovakia in 1992; the post-war small ("third") Yugoslavia that was meant as a union between Serbia and Montenegro was also dissolved in 2006, followed by the independence of Kosovo (2008). This trend is also present in Western Europe, with "breaking-points" periodically looming in UK (Scotland), Belgium, Spain (Catalonia), not to mention Brexit as a case of a separatist trend at EU-level.)
The one decisive reason I think it was already pointed out in a simplistic way that triggered down-voting by an answer that simply mentioned Russia.
The recent situation in Ukraine with the occupation of Crimea and the war in the Eastern part of the country clearly draws the map of the larger geopolitical context. It is not that simply everything depends on Russia, it is the larger deployment of forces that are at work in the Western part of the former Soviet Union which was decisive after 1991 and still represents the decisive factor. This larger context can be described as the geopolitical confrontation between Russia (especially with the Putin era) and the West (also the EU, but especially NATO and the US).
The US administration may prove more or less isolationist and the US influence may become less important in the Near East at times, but that is compensated in Europe by the pro-Western trend in Ukraine, as the US/NATO military presence in Eastern Europe is stronger than ever.
The unification between Romania and the Republic and Moldova cannot occur outside the movement of the boundaries of influence between these two opposed camps, and only with the full appurtenance of both states to the same camp.
This never happened after 1991. In the context of instability immediately after the fall of the URSS there probably were a few months when the unionist forces tested the situation and tried to decisively turn the balance, but the Russian reaction was prompt, and the Transnistria War ensued. Only recently the strong Russian influence in the Republic of Moldova receded somewhat in political terms, while in military terms the Russian presence in Transnistria has not changed (the Russian base there, although itself surrounded, is part of a force that, along with those of Crimea, physically encircles Ukraine).
As for the two states to find themselves in the same camp, this can happen in just two cases:
- the geopolitical conflict between Russia and the West&US in Eastern Europe needs to arrive to some sort of solution (and only then we will be able to judge on the importance of the secondary reasons involved in the non-unification of the two states);
- or, the West would have to escalate the conflict to a point where unification of the two states becomes an instrument (against Russia) in this conflict (a highly improbable scenario for the moment).
The present situation does not satisfy any of the two opposing conditions. The conflict in Ukraine is close to a cold war or it involves from at least the pro-Western party an effort to isolate the spread of the conflict. The initial scenario where the conflict would spread to larger parts of Eastern Ukraine and even of the South and West (Odessa) closer to the Republic of Moldova and namely to Transnistria and the Russian military base there has become improbable.
A comparison between Ukraine and the Republic of Moldova may help better judge the importance of all the factors involved (there are great similarities concerning the importance of the Russian and other minorities and the economic fragility, and factors that seemed decisive in keeping Ukraine in the Russian sphere have suddenly became less important, although they are more significant than in the small Romanian-speaking country).
Ukraine has to pay its effective independence from Russia through a chronic war, the end of which is uncertain, but which has triggered a strongly anti-Russian trend at the political level. But it is hard to say how long that trend will endure and how the war will impact the political situation. The Republic of Moldova has already followed that logic in 1990 when a war broke, but then has avoided war (just like Ukraine until recently) by avoiding a strong anti-Russian politics.
The recent violent events have highlighted the main lines of the geopolitical landscape that was and is deciding the situation of the Republic of Moldova after the fall of the Soviet Union.