Nexus was not a late addition. The goal was the Thirteen Primes... and as
@Sabrblade said making one of the Thirteen a last second addition makes zero sense.
I seem to recall a brand team interview where one them (I want to say Evan?) said that he was originally going to be a Leader but some stuff got shifted around and he ended up as a Voyager. This opened up a spare Leader slot which is how Unicron Soldier happened.
Anyway it seems like they were struggling to see how Nexus would work given the frame system modern Combiners have to adhere to.
In retrospect they should have just had Nexus and a frame be one of AotP's Commander releases with his four limbs spread across a year's waves. And just saved Onslaught for Age of Evolutions year one as a bridge between AotP and AoEv.
Still, they did what they did and are trying to fix it after the fact. The shame of it is that Nexus is a great figure in his own right and not nearly bad enough to deserve the hate. He's even accurate to some versions of the mythos (IDW, TFO) where he is just a normal sized dude.
All of this just highlights the big downside to the current Combiner system, however. Torsos were Voyagers back during Combiner Wars, so they could be pumped out pretty steadily and getting repaints for things like G2 releases or Baldigus/Ruination wasn't that big a deal.
But now Combiner torsos are pricy Commanders which only get one slot a year. It means they can't do more than one Combiner at once (being able to do two would have helped considerably with Nexus) and getting repaints are tricky because you need to find a "slot," ie a retailer willing to carry a pricy item that may take up inventory space for months on end. They still don't have a spot for G2 Motormaster.
The whole system just limits what you can do and it means either dedicating the slot to Combiner torsos for years on end or just not doing Combiners for a while and leaving gaps in peoples' collections.
And now they're stuck with a Voyager torso who will get limbs who can't combine without someone else's frame. The limbs aren't that huge a deal, you just need four Deluxe slots... but if they do ever want to complete the set... how will they manage it? What's the pitch to retailers going to be for something that's JUST a frame?
This whole thing has been kind of a clusterf**k. I'm quite relieved I like Nexus as he is... so I don't feel like I NEED to compete his combined mode... but still. Backing themselves into the corner of "our Combiner torsos can only be one a year $90+ releases" did no one any favours.
My guess is that the original plan was for the 13 Primes to come out across two years instead of one but that just speculation on my part and next year we'll likely see retools appearing of some of the deluxes and voyagers
AotP is a two year line.