So after looking over the Rogue's Galleries on the Elites extensively, the following thoughts came to me.

1. The timeline for the Elite Clockworks' creation seems to me to be:
a. Toymaker creates Phule
b. Toymaker creates Bishop
c. Toymaker creates Kane
d. Kane creates Rooke
e. Kane creates Deacon

Notes: First, we have no information on Good ole What's Her Name. Second, the Rogue's Gallery was unclear-Bishop may have been created by Kane, or not--we, and the npcs in game, are unsure. For the purposes of this post, I am going to assume that the toymaker made Bishop. This is because I think I have identified a trend, which I will elaborate on below.

2. The Toymaker seems to me to have been shooting for one trait above all else-mental fortitude. And mental fortitude in many forms. It appears to me that he intended to create Phule to be extremely smart (when they reference his black form as like Kane; this part seems a very focused tactical thinker). But he also intended him to be Creative-to allow him to outthink any problem that came his way. So he gave him a duality, which turned into a split personality, and unfortunately insanity. So Toymaker revises.

He then creates Bishop-still intelligent, but less able to sympathize with the enemy than Phule-so less likely to go crazy right off the bat. However, he does have a vulnerability that the Toymaker was wary of, especially given how Phule turned out-his emotional attachment. He is emotionally very present--he flees from us, reappears on a whim, flees again, returns again, flees again. Almost against his better judgement. Like his fear, his irritation and above all, his curiosity, are possessing him. Which brings me to another point: He is relentlessly curious, which allows for great innovation and creativity on his part-but puts him in danger. An example would be Beachhead- after fighting us in Central Core(1st time), instead of raising an alarm, and trying to summon a huge force to subdue us, he wastes time observing us. He realizes what we are doing, because as Supreme Curious Genius that's his job--and so he lays out defenses-but they are extensive as opposed to exhaustive--that is to say, he has us fight a bunch of small battles with clockworks to see how we work. Perhaps, as a being controlled by emotion, he expects us to be emotionally drained by the time we get to him, and for this to affect our ability to fight. Regardless, it doesn't, we defeat him, and he flees again-in a sense his emotionality keeps him alive, but perhaps Toymaker (or whomever was controlling him) didn't want someone who would run away until the very end-someone who would have not fled the first 4 times that Bishop did. So he revises.

And he creates Kane-and Kane is definitely distinct from Bishop and Phule-he is supposedly a genius, as everyone will assure us. But he is about the most emotionally cold villain I can think of. (running out of characters ) to be continued...

(Part 3)
We defeat distressed out of his mind Rooke. He has a chance to run, but finally succumbs to the emotion and attacks us again. And fails.

4. Good 'Ole What's Her Name-we don't know, well, anything about her. But I believe whomever her creator was will be very symbolic and telling about both her character and her fate. If Kane created her, we can expect her to be emotionally detached as well, and we may assume that she will perish at our hands given the current trend. On the other hand, if she was created by the Toymaker, I'd expect her role to be less defined (Mad Scientist and....Whatever The Heck Phule Does are not as specific/militarily focused roles as General/Spymaster are), expect her to be more enigmatic, animated and emotional, and perhaps...expect her to survive multiple encounters with us as Bisphop and Phule have done.

Needless to say, I'm a bit obsessed with the Armada. When does Book 15 come out again????

I think Kane was first according the puppet show.

Kan The Destroyer on Oct 5, 2015 wrote:

According to the Puppet Show, sure... but that's being told to us by Avery, and thus has his limited knowledge and bias built in, not to mention it's one of the earlier ones and so is prone to sensationalism (so players don't quit early on). "First of the clockworks" sounds cooler than "A really important clockwork."
Another thing you might consider is that when Avery says "First of the Clockworks", he might mean "Leader of the Clockworks/First in Command of the Clockworks" as opposed to "First Created Clockwork".
Also, I wasn't working off just the Puppet Shows, but the Rogue's Galleries as well. This is just how it appeared to me.

Excellent analysis, I'm watching this topic.