I figure Brainiac should have an obviously different technological level from Kryptonian tech-either somehow more advanced or realistically lower. Maybe they can play with the idea that Brainiac has probes that advance across the galaxy and explain that they all travel without a hyperdrive, so the Brainiac we encounter in the sequel has been on Earth for a very long time and mostly uses software to physically act on the world.
Picture an ancient machine with nanotechnology hidden inside itself that can possess a host body if it needs to and has been acting to fulfill an ancient program from Colu. And while his technological database is centuries ahead of Humanity, he desires to gain Kryptonain technology as well.
So I figure a good plot would say that this Brainiac probe has been waiting for Earth to reach a certain technological apex so that it can run a terrifyingly effective wargame to see how humanity would react to a war involving every single resource on the planet. He does this because the Coluans programmed him to try this on every single sentient planet he could in hopes of finding allies against some great unspeakable threat that can recruit an entire species to wage war on itself in planetary suicide. Notice the above is only suggested later.
As STAR Labs, the Russian company Rocket R.E.D., Wayne Eterprises, and LexCorp begin to experiment with their own nanotechnology and advanced cybernetics, Brainiac begins to set his plan into motion. However, he believes that Superman will contaminate the test with his capabilities, so as LexCorp scientist Milton Fine he makes a deal with the antagonistic Lex Luthor to unleash Lex's future soldier John Corben against Sperman as a distraction.
Of course, Corben is defeated easily at first and abandoned by the cynical Luthor, so Brainaic fully upgrades him into Metallo, complete with transhuman angst and a sliver of kryptonite. When his war game fails, he decides to save a few humans for experimentation and kill the st with a nano-plague, but Lex and Superman manage, through teeth clenched team work, to stop his plans, with Lex securing both Brainiac as a program he can use and the kryptonite.
Also, the threat Brainiac keeps testing against? Darkseid.