As far as I can tell pre-registration of scientific studies has been proposed as a solution to three important problems with the current model of scientific publications: replication, negative results and p-hacking. I personally think that it is great that this format will allow more replication studies to be undertaken and more importantly it will enable the publication of replication studies even if the results are negative. This will be of clear value to the field.
All my reservations about pre-registration concern p-hacking, more specifically how this has been 'sold' to the community. Pre-registration is a solution to the problem of p-hacking. However, those promoting pre-registration have often argued that pre-registered articles should somehow be considered "more truthful" than those that have been published by the traditional route. I strongly disagree with this kind of statement. It is true that pre-registered studies will not be p-hacked, however not all studies that are not pre-registered are p-hacked. The danger of promoting pre-registration as more 'truthful' is that the community will stop believing results from someone who has decided not to pre-register for whatever reason - maybe they wanted the freedom to publish their results wherever they wanted, maybe they did not want to deal with reviewers who might disagree with the experimental design or maybe they just wanted to start the study rather than wait for months before approval.
P-hacking is clearly a problem, particular as it can occur subconsciously. However, at the current time I can not see how pre-registration will work in practice to prevent p-hacking and I worry that it has been promoted in a way that potentially will denigrate equally good science that has been published via a different route.