I posted this earlier, but I thought it merited its own thread. IMNSHO, it keeps the Shivans alien while explaining many of their actions.
I. ORIGINS AND MOTIVATIONS
The Shivans evolved in a rapidly-changing environment that encouraged copying stronger life forms (if you can't beat 'em, join 'em), assimilating weaker ones which were sufficiently malleable (by directing their evolution), and destroying weaker ones which were disruptive or less malleable. These became their core motivations, even after they had eliminated all competition and moved on to other environments, where the strategy was no longer optimal.
II. THE ANCIENTS AND THE GREAT WAR
The Ancients were not malleable, and they were destroying more malleable species which could otherwise have been assimilated. In contrast, by working together and pooling resources, the Terrans and Vasudans demonstrated their ability to merge technologies and adapt. Accordingly, the Shivans launched a subtle, long-term program to manipulate Terran and Vasudan progress, partly by confronting us with increasingly powerful threats.
III. HE WHO FIGHTS WITH MONSTERS
For example, the Lucifer gave us beam technology; in FS2, when we were stronger, the Shivans deployed many more beam-equipped warships. By the end of FS2, we are using or learning to use Shivan technology (shields, beams, Kayser weaponry) and tactics (adaptation, subspace maneuvers, acceptance of casualties). We are ever-so-slightly closer to being assimilated. Note that the Shivans could destroy us at any time (e.g. via the Lucifer fleet's still-unknown point of entry), but choose not to.
IV. THE COSMIC SCALE
The GTVA is one of many societies that are being groomed for assimilation. The Shivans are managing a vast "educational system" for various life forms, some more Shivan than others. The Shivan forces in any given classroom are uniquely suited to their students, and are somewhat different from the "true" Shivans at the center: the ones who pull the strings and maintain the records. After billions of years of adaptation and assimilation, the Shivans have become a great average - sort of an ideal to which all life forms gravitate, willingly or otherwise.
V. ADMIRAL BOSCH AND CAPELLA
Admiral Bosch surprised the Shivans. His communication with them demonstrated an understanding far beyond what was expected, given the GTVA's primitiveness. He was such an anomaly, in fact, that the local Shivan forces didn't know how to respond, so they sent him on a high-priority flight to their administrators. The destruction of Capella created a temporary connection to the main Shivan systems. It was merely a time-saver, with side effects that the Shivans deemed insignificant. They could have gone a longer, less spectacular way around, but they couldn't be bothered.
VI. FUTURE POSSIBILITIES
The Shivans could view Admiral Bosch's game changer as a dangerous aberration, a monumental achievement, or even an insoluble paradox - respectively resulting in our immediate annihilation, an acceleration of their program, and their going berserk or ignoring us altogether. On the GTVA's side, a suicidal and extremely well-informed strike force could follow the juggernauts into the belly of the beast, during the final moments of FS2.