Speaking from the nearly-clueless new-guy perspective, I cannot fathom the thinking behind these latest changes to science labs. Just how long is it supposed to take to knowledge raid now? And even after all the micromanagement, time and expense it gives the AI bonus reinforcements? What problem did this solve?
And on a related note, I don't understand the desire to make just about everything that's supposed to be helpful a double-edged sword. Distribution Nodes, ship caches, and golems all cause AI progress. One reliably optimal strategic option is to ignore them all. Was that the design goal? I'd say the galaxy is already a pretty unfriendly place already without tainting nearly every possible beneficial option with negatives. Even time is against us, after all.
All the info you want is here:
http://arcengames.com/forums/index.php/topic,5522.msg40222.html#msg40222Rest assured, we're not morons and it was solving a rather serious problem. Also, if you're having to knowledge raid a ton, there's a larger problem at work here.
Regarding why everything has both positive and negative consequences, it's because it creates opportunity cost. In a typical RTS game, you can just spam the best unit, build a bajillion of them repeatedly, and smash them against your opponent until your opponent is dead. Next game, repeat. Chess is specifically really interesting because every turn you get
one move. Moved that queen, did you? Then you can't move your knight, which maybe then gets taken by your opponent. Players choose to sacrifice the tempo for material, or vice versa. Players trade material, in hopes of trading up. And so on and so forth.
Many RTS games turn into games of speed and reflexes simply because there are no such checks and balances. AI War is built around the idea of making that sort of Chess concept work in a realtime context. So that's why there's some sort of penalty for... everything. Each thing you do means that there is something else you couldn't do. Otherwise you could just do everything, if you were prepared to spend enough time. There are still a few players who do that even with AI War, but that's really hard to do and most don't (or don't at the regular difficulty levels).
Regarding distribution nodes, those are specifically a "candy" item -- they're there to tempt you, and they can be minorly helpful, but mostly they rot your teeth. Again, that was something players had specifically asked for (like some form of change to knowledge raiding, there's a monster thread about that). The ship caches are a lot more useful, but only in the right context. And that goes back to my central point: you don't just pick up goodies because they are there. You have to actually use the gray matter and decide which goodies are worth the costs of taking them, and when. Otherwise there's not much strategy in a game like this...
Hope that clears things up a bit!