September is heading to back end of peak season but still fine.  The
diving is very good (but not a place for novices - no idea if this
applies or not) but nothing much else to do although the (one) resort
does have pool.  They are also strict with limits and check DCs
sometimes so stick with the limits they prescribe.  The big claim to
fame is the schools of hammerheads.

Getting there is a bit of a pain, small plane out of Kota Kinabalu which
isn't the worlds greatest airport to start with.  Not sure where you are
coming from but if you have several hours in KK then probably worth
getting out to the Tanjung Aru for some R&R rather than hanging around.
 When I went to Sipadan earlier this year you had to clear in and out
of the airport anyway so no real extra grief to leave completely.