From what I read, he came up with the concept of the Junction system (and Triple Triad) and then was pulled early from the team to work on FF Gaiden which eventually became FFIX. Things like the Draw command were added by the VIII team after he left so things may have turned out differently had he stayed on. He also worked on Chrono Trigger between VI and Tactics as a co-director.

A supposed translation of his interviews from the FFIX and XII Ultimania's also goes into detail about what he contributed to games like VI, CT and IX. He's apparently the go to guy for merging gameplay with story scenes cause he thinks just watching a story scene unfold gets a bit too boring so things like the Opera scene, the Banquet with Gestahl, Crono's trial, and Zidane and Blank's fight scene are examples of him trying make the story sequences a bit more interactive and immersive.

Considering his accomplishments, I'm actually surprised he wasn't tapped to be the lead of the main FF development team instead of Toriyama. Though it's probably because Kitase is the head of Division 1 while Ito was given his own division. Interesting enough, when Sakaguchi was asked recently who at Squenix could make Final Fantasy into a leading series of the genre, Sakaguchi said Ito.

I wonder what he's been doing since FFXII International though? I mean he hasn't been on a major project since 2007.