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Pews teach the lay people to stay in their place
In teaching us to sit back and relax, pews give us the impression that any inconvenience, much less suffering no matter how slight, is foreign to the Christian life.
Pews destroy the traditional feeling of freedom in church. With the installation of pews, we are no longer "bothered" with all the moving around which used to take place. You know, grandmothers lighting candies, children kissing icons, and the worshippers gathering around their priest like a family gathered about their father.
You also, I believe, pointed out that pews are a "Liturgical innovation" (or something to that effect). As far "Liturgical innovations" go, you will find that many practices we currently accept as common and normative (e.g. taking Communion with a small spoon) would have been quite innovative and even un-canonical in the days of our Fathers (depending on jurisdiction ofcourse).