Man if Hideo was half as good as Shirow...
Shirow never made the mistake of showing the men behind the curtain. His characters are very much soldiers and pawns that operate at their level far from the actual motivations of the puppet masters. There's no pussyfooting around the fact that they are spooks and shady killers: Deunan would never make a stupid 10 page speech about life, war, control of information and everything else. The characters are much more down to earth (the Knute / Briaeros couple is genuinely a superb and subtle relationship). Shirow is also not shy to show Japan (in GitS) as a proactive covert political force despite the constitution, featuring the Kouriles island and uneasy relations with China (in the series at least). Japanese / Olympus politics are dirty but the characters never derelict duty or go full distinguished mentally-challenged fellow like Big Boss, they always serve their political masters, system or order. He's much more self aware than Kojima, and I never felt he had the same love/hate boner for the US or the West, the rest of the world never features too prominently, even if he took the care of thinking about how it all stands post WW3. A lot of the Otaku culture have this military and destruction fixation but few are as oblivious than Kojima about it. Anno is a Navy guy and in Gunbuster you have those weird hints of a revanchist fantasy of Hawaii being Japanese and the future space Navy using Imperial uniforms. Otomo is all about fight the power but he reflects on post WW2 Japan and has no illusions on its hypocrisy or the fact that the alternatives will be crapsack for a long while.
As a sidenote I read a good study somewhere where anime creators themselves said that the Aum chemical attack and the 95 Kobe quake made them more sober vis à vis their apocalyptic hard-ons. It was suddenly much less cool and awesome now that they had a taste of it. I don't know if this is what happened to Shirow, but he lived in Kobe and the break in his career is around that time. At the very least I recall to have read that he lost part of his work and that might have prompted him to reconsider his career.
I am always bummed by the unfinished Appleseed tome 5, the beginning of it is pretty awesome.
Edit: I also never felt Shirow was as crass as Kojima with his women characters, despite being from the same school of pretty ridiculous outfits, statuesque bodies and perv tendency as per his current work. Maybe because they always felt like characters.
Edit: Doesn't help that Big Boss is such a non character (from MGS3). I mean the dude is a fucking copypasta job of Snake appearance wise with wangst. We're told a lot he is charismatic and deep, but I don't see it. (Total disclosure here, I only played MGS3 and GZ, not the other titles featuring BB esp. on portable, so I may be a moron that will his foot in his mouth and all that).