NinjaLA: my only complaint so far was that when I was grinding the sakkra to dust, they refused to make peace with me. so I obliterated them for stubbornness :D
I actually had a very similar situation - I intentionally left the Sakkra with a single planet and kept destroying any ships they made to see what they would do. They never even tried to contact me!
In MOO2 this type of gameplay usually led to any species begrudgingly seeking a truce, often with a lot of nice incentives for me, but the Sakkra never did. I approached them and offered a truce multiple times, but the conditions they wanted to impose upon me were always ridiculous - most (if not all) of my wealth, a huge annual payment and a handful of star systems.
I had a similar war with the Mrrshan later in the same game, and once they got down to a single planet they offered peace - but nothing else. I'd like it if the AI recognized who was actually winning the war, rather than acting as though we're totally even (or being in complete denial and considering themselves the ones doing me a favour).
The bizarre contrast is that, for any of the species that I
wasn't at war, once they were afraid of me (as in, the relationship status is marked 'AFRAID') I could demand just about anything from them and they'd hand it over. Tech, money, treaties, even star systems - so long as I was wiping the floor with somebody else, they knew who was boss.
(Note that this doesn't mean I'm not having an absolute blast with this game! :D)