The Scottish Government didn't 'chose' Abellio. The Scottish Government set out an Invitation to Tender document which set out various requirements for the new franchise, and the way in which bids would be judged. Various companies submitted bids, and Abellio's scored the highest according to the process laid out in the ITT. At that point, the Scottish Government have essentially no choice but to award it to Abellio. If they didn't, they would open themselves up to legal action, and they would lose.
Abellio wasn't even the cheapest bidder. National Express bid less, but Abellio had the highest bid quality score of anyone and this was enough to overcome coming second in the financial stakes. Again, this was only because the ITT process had set out the bid scoring mechanism and explained how quality accounted for a significant percentage of the overall score.
These things are really, really hard. On one level, you want to have as ambitious a programme for the railway in Scotland as possible. On the other, that ambition involves risks. It would be very easy for the Scottish Government to get a franchise which was bang-on guaranteed to run reliably all the time, but only by artificially restricting the capability of the railway. Is it better to have a superior service 90% of the time or a middling service 100% of the time?