I haven't fully looked into the espionage system but I have been hearing that you need highly trained spies in a rivals territory in order to obtain fleet composition information.
I've only done a single quick playthrough of version 3.01 and I was happy to see that they had finally added a sort option for colonies; the industrial districts and forge/factory changes seem like an interesting change, though I'm not a fan with what they did to Ring worlds or the Ecumenopolis planets. The population growth system though seems to be making a lot of people on the forums unhappy (I didn't like it in version 2.2-2.8 either however)....myself I played version 2.1.4 straight after 3.01 and found that I'm still a fan of the working sector AI, tiles, population growth and migration mechanics...it is a simpler system but feels more polished and functional to me.
Starsector is in another dimension in terms of support and updates, so I do feel a bit spoilt with the regular changelogs. It's also rather impressive that it wasn't called version 1.0 several versions back and all subsequent updates made into purchaseable DLCs. There are changes that come about that I don't like (I really like the presentation of the skill system in 0.95a, just not a fan with having to purchase skills in a sequential order to unlock other skills) and some that I worry about (I wake up in a nervous sweat with a new update doing a quick CTRL-F and 'Apogee' to make sure it doesn't get nerfed as my favourite exploration ship), but overall I find the changes as a whole are always positive.
I also like how much more freedom there is to be critical on these forums (and how often feedback is given in response)...Paradox is not a nice forum to post a contrary opinion (though it does mean that those brave enough to post have polished their thoughts well).