I believe the point of contention with the GREAT Regiments is that it implies we indoctrinate clones to fight, stripping them of agency and putting us in a totalitarian light. This, in large part, is because the
initial proposal basically says this outright. However, I personally believe that all design proposals are irrelevant the moment the dice are rolled. Look at every AR ever. In the vast majority of cases, the result is not the same as the initial proposal, thus we can safely disregard that from further discussion.
The next point of contention is in the
project result, specifically the line "The GREAT regiments are born to a life of service, as most Gaians are in one way or another". Depending on how you choose interpret this, it could be a philosophical statement about how all citizens and institutions serve to further their country, in a paraphrase of JFK's famous remark. Or it could be seen as further proof that the soldiers are indoctrinated from birth.
I personally choose to interpret it in the philosophical sense. It is, after all, a single comment by the GM. It is perfectly possible, after all, for children to be studied as they grow, allowing their carers to identify future career paths they will be both effective in and enjoy. After all we don't want people to be stuck in jobs they dislike or aren't good at. We can't afford that sort of inefficiency at this stage. From there they can present the child with all the guidance and assistance they need.