I don't like to examine fiction too often from the standpoint of what it was I think the author or authors were trying to do. It's sort of presumptuous and I am normally wrong. But I will try here anyway for a second before getting into the meat of my review because, well...I don't know. I'm just going to.
Crossovers between major books in a continuity are nothing new. DC and Marvel make regular huge bucks off of them, so it's no wonder IDW tried as well. My hypothesis is that this particular story came about as trying to clear away some of the rubbish that existed from the run of the previous writers—most notably the "Dark Universe" idea.
I could spent a lot of time on how much I dislike any alternate reality storylines in fiction, but for this particular scenario, let me just put it this way: the Transformers exist as a space-faring species that are able to, it seems, cross the entirety of the universe with ease. And the only thing that they are able to reasonably combat and engage with has to come from a completely new universe? This sort of splitting into alternate realities is something we almost expect from stories set on Earth, restricted to Earth-creatures who don't hold dominance over star travel. But the Transformers do, and so requiring them to fight something from another dimension (and to fight THEMSELVES from another dimension) is a far cry from the fun swashbuckling tales from MTMTE and the engaging political intrigue from RID. But, maybe that it's a far cry from these was part of the point.
Anyway, the palette is cleansed, now. The Dark Universe is done. This big storyline is not without its merits (not by a long shot). I read all of them in the space of about a day. I enjoyed the many competing paternalistic influences, from the benovolent (Pax/Prime) to the irrational (Rodimus) to the nasty (Nova) to the indeterminable (Megatron) to the irascibly moral (Bumblebee). With so many tugs in so many different directions on the ethical latitudes of the Cybertronians, it's no wonder they've been in perpetual war. Everybody makes a certain sort of sense, which is terrifying considering some of their objectives.
All anyone can really agree on is that Shockwave is a bad guy, and even Shockwave is only bad (and specifically so) because he is a victim of his government's class-based mutilation of his rights. There is good exploration here of the manner in which we create monsters, in that when we make our punishments as terrible as possible, the things that go on to survive them become even more terrible in response. I mean, I know it's the thing to label Shockwave as some emotionless monster, but his goal is literally to keep things in stasis forever. Imagine that; a guy who has been horribly disfigured by his government wanting that to become literally impossible to ever happen again.
The thing I like about Transformers is the mirror that it holds up to ourselves. This is what I like about all science fiction. If there's a mirror here, it's not entirely friendly; but at least, it seems as though the Cybertronians are learning their lesson a little bit by the end of it. We can only hope the same.