Given the Scottish Parliament was re-established by the first New Labour UK Government (1997-2001), proportional representation (PR) was an unusual choice of electoral system for two reasons. First, Scotland had consistently returned an outright majority of Labour MPs to Westminster and, second, PR was a policy closely associated with the Liberal Democrats (LibDems). Using a simple first-past-the-post constituency system, Labour would have easily achieved an outright majority in the new Scottish Parliament.
However, any system which gave the Scottish Parliament an administration based on a clear majority also gave it power in the form of a strong mandate. The latter was fine so long as unionist parties were in the majority, as they would not use such a mandate to pursue further constitutional change. There was a risk that any system which easily enabled parliamentary majorities could lead to a pro-independence government in the future.
PR was a means of making parliamentary majorities unlikely, rule by consensus the norm, and coalitions a permanent feature of Scottish Government. This made the Scottish Parliament 'weak' (where no party ruled on its own) compared to Westminster (where single party majority rule was the norm). Unsurprisingly, the first two Scottish Parliaments of 1999-2003 and 2003-2007 were ruled by Labour-LibDem coalitions, and the Scottish National Party (SNP) lost political ground during this period. It looked like devolution had been successful in stopping the nationalist tide and the drift towards independence.
It is also important to recognise that PR was already an established model in different European contexts and in the first re-convened Scottish Parliament at least, it facilitated a rather different looking multi-party parliament from the one that characterised the Westminster Parliament.
Take your learning further
Take a look at a breakdown of parliamentary seats won at the first three Scottish elections.