Comments up thread hit on why this episode felt a little "off" to me; this was very much a series one RTD episode. I wonder if the cause is budget. Series one did not have a large budget, and that contributed to its feel as much as RTD did.
Doctor Who has been blowing through a good bit of money lately (the most noticeable being the second major TARDIS overhaul since Moffat took over). "The Bells of St. John" was a low budget episode; the question is how many more low budget eps we'll see in order to cover the spending gap.