He was unpopular in his country and probably unpopular with the Germans.

Being of the disposition he was, it is very likely that the Kaiser found it difficult to bend him completely to his will.
Being a stumbling block in the way of German aims, is it not reasonably probable that Germany desired to get rid of him, thus leaving Austria-Hungary completely in the power of its tool and puppet, Francis Joseph, and in the event of his death, in the power of the young and suppliant Karl; another instrument easily bent to the German will?
The wife of the archduke, assassinated with him, was a Bohemian, her maiden name being Sophie Chotek.

She was not of noble blood as Bohemia had no nobles.

They had been driven out of the country centuries before and their titles and estates conferred on indigent Spanish and Austrian adventurers.

Not being of noble birth, she was but the morgantic wife of the Austrian heir.