No, the Emperor wanted Azel because she could control the Tower. The fact that she was designed to destroy the Tower by interfacing with it is irrelevant. The only thing the Empire cared about was harnessing the Tower; Azel could help the Empire accomplish this.
Read the beggining of your last post Geoff 
If you consider Abadds plan you could think that at least Orta would be able to link with every Tower - and to hand down this ability Azel would have to possess it herselves.
Eh? All Abadd wants Orta for is her reproductive ability no? What do Towers have to do with it, why would she need access to all of them… Why would Abadd seek that…
Orta is a showbag - reproductive and queen of the towers.
Of course, that’s only another theory.
But I don’t see why you think Abadd wants access to all the Towers… I suppose they could help him in his task of creating his army of drones by using Orta but then again, most/all of them are deactivated…
Terraforming abilities can’t hurt in an upcoming war.
But the towers are inactive… The DV made sure of that… Don’t think Abadd can just move in and press the light switch and all will be powered up…
Sorry to jump back halfway through the topic:
What struck me was that the rebels might not literally have modified her; of course, it’s unclear if that would be possible or if they’d have the knowledge to do that, or even the means to do that. But if Azel wasn’t totally completed when they stole her, that would imply that she wouldn’t have been put to any purposes or started any duties yet. If she hadn’t yet been given a programme to perform, that might simply mean that she was a blank slate: receptive to whatever tasks that the rebels could give her.
Not that that little sub-theory really changes anything, it’s just something that occured to me.
Yeah, I think Azel was stolen because she was already equipped to interface with a Tower. Perhaps the Uru labs focused on contructing higher end drones, which is why the scientists there ran into some problems.
Zadoc the compiler said that to control the Towers, Azel’s intellect was enhanced, which gave birth to human emotions. However, he doesn’t say who enhanced her intellect in that fashion.
Then they’d “cancel” Atolm from her though… Unless you think Atolm was stolen as well…
I’m thinking they could have taken her overnight, modified her, then snuck her back inside without anyone realising anything was wrong…
In order to control the Towers, she was given superior intellect.
I know it’s hardly conclusive, but as we’re informed that she was literally created to interface with a Tower I get the impression that she was given this superior-to-a-normal-drone intelligence by her original makers.
That’s exactly what I think happened. She had not been equipped with the device the Ancient scientists mentioned. I think this device kept their thoughts under control, like we see with Abadd.
If she was stolen like that why didn’t the Ancients change Atolm’s duty of protecting her and give it another drone rider to replace Azel? Or was a full dragon stolen as well…
That’s one of my best guesses. It doesn’t seem suggested that Azel found her way back to her creators, and as Atolm was both with her in the Ancient Age and stored with her at Site #4 it seems that the rebels possibly nicked him too, or that they just created him themselves.
Maybe the creator of Azel him/herselves made it possible to steal her, when he/she changed sides - i always liked the idea of Azels creator looking similar to her - designers tend do that. 
Then Azels enhancements were activated, maybe functions that lay dormant because they were only experimental and not needed for her task.
Atolm - hm, that’s a little harder. I think a popular theory is that Azel was able to call her dragon and awake it from its sleep.
If you’re still interested Gehn, I think we’ve got another reason to believe that Azel could only interface with the Tower of Uru. We know that there were a whole host of Towers scattered throughout that part of the Continent, and we know that most Towers were in some kind of “standby” mode in which they weren’t defending themselves or churning out pure-type monsters. However, the Seekers’ plan for Azel to open a gateway to Sestren involved her going to that specific, recently activated, violently aggressive Tower and opening the gateway from there.
It might be safer to assume that Azel could only interface with that Tower’s systems. Unless of course the Seekers didn’t know anything about any of the dozen or so other Towers in the surrounding lands, but that seems less likely given their good knowledge of the Towers (and lines like “the Towers are located throughout this world; to destroy them all, it would take decades”).
You got a good point there Lance
According to the Tower map there were Towers located much closer to the Empire than the Tower of Uru; why didn’t the Empire discover them?
Also, how the hell did the Empire locate the Tower of Uru anyway? The Imperials couldn’t have scouted the region since the area around the Tower was blanketed with thick fog. The Empire must’ve found an old map pinpointing the Uru Tower’s location.
Remember that at the time the Empire didn’t even know what a Tower was, though - Craymen may have done his homework, but the other Imperials seemed convinced that a Tower was some sort of ultimate weapon they could just turn on and start blowing their enemies up with. They never showed any indication of knowing that Sestren existed either, so it looks safe to assume that they knew much less about the Towers than the Seekers.
My best guess is that the Towers near the Empire were incredibly well-concealed; swallowed up by geological changes and sunken beneath inland seas. The Empire didn’t really know what they were looking for, so it’s likely that they simply didn’t find it.
EDIT: Remember that it took them eighty-nine years to notice the Tower poking out of the sea off the coast of their capital…