I will be discussing this topic in my Northern Wei series articles. The Weishu gives this comment on his administrative abilities:
"太宗即位,修廢官,恤民隱,命南平公長孫嵩、北新侯安同對理民訟,庶政復有敍焉。帝既練精庶事,為吏者浸以深文避罪."
"Taizong ascended the throne, repaired abandoned offices, relieved the people's suffering, ordered the Duke of Nanping Zhangsun (Baba) Song and the Marquis of Beixin An Tong to manage the disputes of the people, and common governance was restored and expressed. The emperor was proficient in the various affairs, and those who served as officials gradually because they were well-versed in refined writings avoided faults."
To me, this seems to be talking about a well-run administration. Tuoba Si does seem to have been strict with his officials, as another biography mentions that he frequently punished their offenses via canings, but he never seemed unfair or excessive to me. As well, he does seem to have treated the common people well, providing relief and listening to their concerns. I don't think his administration was cruel. The Weishu also praises him as a virtuous ruler, though these praises were common for early rulers of a dynasty in the book pertaining to said dynasty.
It should also be noted that even though he launched a campaign against Liu Song, the Songshu didn't make out Tuoba Si to be a tyrant, but it did make out Tuoba Gui and Tuoba Dao to be tyrants. This indicates that his rule should have been more benevolent than his father's or his son's. As well, the large amount of refugee activity from other states and the submission of various tribes to him should indicate that his rule was relatively stable and people were willing to live under it, which means it could not have been too cruel.
I agree on Tuoba Gui's later reign. There is no doubt that there was a mental decline in Tuoba Gui and a decline in his administration. However, the claims of the Songshu seem purposefully embellished to defame their rivals. The anecdote about Tuoba Gui destroying his own county because of a prophecy he misinterpreted seems too outlandish, cliched and relying on storytelling tropes, and seems more at home in a fantasy novel than in historical records.
I think that the Weishu records on his later reign should be much more reliable. They had much less reason to defame Tuoba Gui compared to the Songshu. His cruelty in his later reign can be backed up by the noted attempts of Tuoba Si to fix these problems, Tuoba Si fleeing the capital rather than accept his summon to his father, and the executions and demotions of officials as mentioned in records, even if specific anecdotes are exaggerated.
Another record in the Songshu I find too outlandish to be true is the claim that Tuoba Dao was unknown to Tuoba Si and treated like a slave by the palace at age 15 or 16. It makes no sense, as at 15 or 16, Tuoba Si had made Tuoba Dao acting ruler of the state, and the officials all seemed to respect him highly. This makes no sense if the Songshu record is correct, so I suspect it was written to defame him.