[ Wiktionary: ] Etymology From in- + parō.
(with dative) I command, give orders to
I rule, govern
I demand, impose
Because the 3 definitions above matches the meaning that one prepares (i.e. parat) TO or TOWARDS something, should not 'ad'- have been the apter prefix?
How do the 3 definitions above match the meaning of preparing IN someone/something?
There actually is an apparo (ad + paro). The prefix ad- was assimilated and the 'd' turned into a 'p'. The word apparo means to prepare or provide.
As C.M. Weimer commented, in- has an accusative sense which means to or into. There are many compound verbs prefixed by in which carry this sense, such as ingredior, infero, and ineo.
There is another explanation for the meaning of impero. Compound verbs often take a dative, and the meaning of this dative is often related to the prefix. Considero impero tibi, which means "I give a command to you". See how the preposition "to" in the English translation conveys the sense of the prefix? Another example would be absum tibi, "I am absent from you".
So, considering the accusative sense of in-, the meaning of impero is quite logical.
The cases are derived from the parts (and meaning) of the word, not vice versa. Furthermore "impero" can have accusative-like component as well, referring to what is being commanded, albeit this is typically a verb. So to distinguish, the target of the command is probably considered the "beneficiary" of the verb, hence dative.
As to why it is im- + parare that evolved into the meaning of commanding (and not ad- or something else), I can only say that historical semantics are pretty goofy sometimes and we have plenty of similar strange examples in Czech. The metaphor probably comes from parare meaning primarily "prepare", but also by extension "arrange", "contrive" etc. Im-parare may have originated putting this purpose to do something into somebody.
