With a 20-planet map or smaller, you can pretty much take every planet without issue, the AI Progress will never get
that high. Even with 30 planets, you can manage without too much trouble. But on 40 planets or higher, and most specifically on the default 60-80 planet range, you'll seal your own doom if you try to take everything (some very careful and enterprising players are able to work around this on difficulty levels that I think are a little on the low side for them, but for general play that rule very much holds true).
This wiki topic also has a list of everything that causes AI Progress increases:
http://arcengames.com/mediawiki/index.php?title=AI_War_-_AI_Progress#When_To_WorryHellish, you say that it is more grindy to take out every syetm, and I could definitely understand that. However, cog says that it is fairly common to take out everything in a system except for the orbital/warp... this is almost the same thing, no?
He's referring to not taking every system on the map, versus cogs was talking about "neutering" specific systems. Generally you wouldn't neuter every planet on the map, is the difference.
Aside from being more grindy, on a difficulty level past a certain point, it is probably impossible to take all of the planets in a larger map; as the AI Progress increases, the AI forces get significantly stronger. Figure 20 AI Progress increase at minimum per planet taken (and more, really, considering Astro Train Stations, Special Forces Guard Posts, and other AIP-increasing things you'll run into), and you're looking at at least 1600 AI Progress in order to take all the planets in an 80 planet system.
With 1600 AI Progress on difficulty 7, often the waves coming at you will be something like 800+ Mark IV ships at once, every 20-30 minutes, and the AI planets will be incredibly well reinforced with very high-level ships. It's a long way to 1600 AI Progress, but really it starts getting mighty unpleasant at even half that value, which is where I tend to end my games at most of the time. There are a variety of ways you can play, for sure, but to survive the onslaught of a super-high AIP, you have to have really ironclad defenses and manage everything perfectly, and probably also play on a somewhat lower difficulty than even 7.
Also, the warp station lets the enemy warp directly into adjacent systems.. when the ai attacks you, can't they go to any system anyhow? In other words, even if you own a system with no enemy adjacent, can't they just attack you directly when you get an alert about them coming in xxx minutes?
The alerts only come to planets that are adjacent to warp gates -- that's what warp gates do. The smaller bands of "special forces" guys that just wander around in twos or tens, or guys that have escaped battle and are now returning, or guys that are part of a cross-planet attack, can indeed go anywhere -- warp gates are irrelevant for them. But the primary vector for large scale assaults on you is via incoming warps from outside the galaxy, and those require a warp gate. If you kill all the warp gates adjacent to one of your planets, you can be confident that no warps will be initiated against that planet -- though that's not
complete protection, it's protection against the very largest danger.