The main reason for differing degrees of linguistic change over time is language contact, where it matters what the degree of contact is and how different the contact language is. The Saami languages are fairly similar, because they have had relatively little contact with structurally-different languages. Bantu languages in certain areas tend to be fairly similar even with a lot of contact because the contact languages are similar Bantu languages, though in a zone where a Bantu language is in contact with a substantially different Bantu language, divergence is often greater.
As for Maltese, one has to start with the question of what the pre-Arabic language was (if there was a single substrate language), what kind of Arabic was introduced (a Maghribi dialect), how much influence there has been from Romance and English (to the point that Semitic vocabulary is a minority), and what kind of reinforcement there has been (i.e. contact with the wider Arab speaking world).
In the case of Afrikaans, there is a hypothesis (M. Valkhoff 1966, Studies in Portuguese and Creole) that the language has in fact been under subtle contact influence from Portuguese Creole and Khoisan, where the influence is on children and their acquisition of the Germanic language, while being cared for by non-Germanic speakers.