At the moment I am really struggeling about the headrole of the protagonist in the first book (in the current plans the story will be a trilogy) because the main protagonist (a cloned politician) will be born at the end of the first book. There are multiple characters with an important role, but none of them really is gonna play the headrole in the completed story. With the antagonist this is different because he is already alive and will be involved in the first book. Is there someone over here who can give me advise, opinions, or better; titles of book, in case of an organisation that turnes out to be the main figure of a story?
It's possible but I wouldn't advise it. The problem is that you can't really make a organisation sympathetic in the same way as characters are. You have two better options - First focus on a smaller group. Perhaps that's the ruling council or the science team or whatever but either way you have a handful of characters as an ensemble each contributing (and conflicting) to the wider story. Think of how Star Trek works; focused around department heads who are in near constant communication which gives you the space to characterise everyone even when they aren't narrating. Secondly (and more radically) ask yourself why are you writing a whole book of background just to introduce one character? Why aren't you just starting with the really interesting bit? I really do understand how this stuff comes together but you need to be dispassionate. What is this first book doing? You'll have to re-explain and re-introduce everything in the second book so why not start there and give us the main story?
You might also consider switching the ant/protagonists in their roles, presenting the antagonist instead as an antihero.
Would you ever root for McDonalds? Find interest in the malevolent practices of Walmart? Perhaps, but not in the same way that you want to chop off the nose Voldemort doesn't have. In my opinion, no; maybe use a small group and/or a "head honcho" and keep the organization.
Organizations are legal fictions - groups of people. Legal fictions aren't interesting, but the people inside them are interesting. So the book has to be about people - or specifically a team of people - which means it's probably an "ensemble drama," where you have a cast working towards a goal rather than just a single protagonist. This is done in fiction but it's done most often on TV - almost any sort of procedural drama has an ensemble cast model - CSI, Grey's Anatomy, Star Trek, Downton Abbey, Game of Thrones...all of those are ensemble casts without strong protagonists, and they're about relationships. The other thing is that they do HAVE protagonists, they just don't have DOMINANT protagonist - sometimes a team leader, sometimes not. CSI's Gil Grisham and the various Star Trek captains were team leaders who protagged ensemble dramas - other characters came to the forefront and often protagged individual episodes and storylines, but the single biggest storyline always came back to the captain or team leader, who you got the most intimate look at. You can also have a titular protag who isn't the team leader but still functions as the emotional center of the piece - this would be Merideth Grey in Grey's Anatomy, who starts at Seattle Grace Hospital in Season 1 as an intern, then gradually works her way up to Resident and then Attending physician. Her's is the main romance, and the core of the ensemble revolves not around the Hospital but around Meredith and the rotation young doctors who she rooms with in a house (Alex Karev, Izzie Stevens, Cristina Yang, and George O'Malley were some of the early core ensemble). In that case, the housemates were as much of a core as the hospital, with the higher-ups playing important but smaller roles. Downton Abbey also has a very diffuse ensemble, but you could probably argue convincingly that it has a definite protagonist in Lady Mary Crowley, especially as the series wears on. Lady Mary wasn't always dragging the action forward, but she was the center-point from which everything else radiated. The triad of Mary and her two sisters drives the family structure as they age, marry, and bear children - with Mary's romances usually coming to the forefront - and Mary's relationship to her maid, Anna, serves as the linchpin stringing together the "upstairs" storyline with the "downstairs" storyline (of which Anna herself is the protagonist). So, there are four TV examples of how to do ensemble drama with a protagonist who is central but not dominant.
