Sunrise of course for Gundam as well as many others. Bones for some really good series, the only one I can recall is Eureka 7. Ghibli for Miyazaki of course. Production IG is ok, but they haven't made anything lately, they introduced the world to Ghost in The Shell though. Madhouse made "The girl Who Leapt through Time" and they are pretty good. Gainax of course for Eva as well as all the other stuff they've churned out; FLCL, GunBuster, Getsumen Tsukihima (Correct?) and their Daikon Series.
Bee Train is a classic old school studio which turns out great ones like "NOIR"
Gonzo's use of CGI is more of a crutch rather than aid, sometimes their staff uses too much, and they need to bulk up their animation and design teams.
I'm more partial to "Girls in power armor" than "magical Cat-girl Lolis"
The mechanical parts replacing their legs or other parts of their anatomy is not exactly my thing. And recognized by the ministry of culture implies to me they all had it in for the loli aspect over the character development
I mean that, I prefer Mecha Musume, rather than loli/mecha/magical/catgirl musume. I'm fine with a character such as Chise from that one show, but when the body parts are the mecha, rather than the mecha are on body parts like added on, or sprout from, then it it kinda gets weird, for me that is.
Simply put, I prefer the girl to wear the mecha parts, rather than the parts are the girls body.