Well, I know some gates last longer, mainly for dramatic effect. The first one (from Leene Square 1000AD to the Misty Mountains 600AD) takes a long time to pass through, initially, so that the player can revel in the coolness of the time portal (I assume that's the reason). The Bucket Gate also takes longer to pass through, and inexplicably has a rainbow around its edge. Then there's the supergate made by Lavos (presumably) in Magus' castle, Lucca's red gate, and I remember seeing a green gate somewhere, I think...
My point is, there are a whole bunch of anomalous gates, and none of them have any real in-game explanation for their differences.