Thank you very much for the feedback guys.
Bali: Is it still worldclass? You mentioned diver traffic, does it impact the diving and are there enough sites for a week's worth of diving, with a day or two here and there to explore topland? Also, I've heard the water temps can be on the chilly side in Sep/Oct, is this something to be worried about?
September might be the warmest waters in Bali, but it really depends on where you dive, for instance a skinsuit would be ok for Amed on the east side but thermoclines will freeze you in Candi Dasa or Nusa Penida...
Crowds : avoid staying in the Kuta/Sanur or Ubud area. Settle the closest you can from the dive sites : Padang Bai area is quite a good trade off if you're not looking for luxury, it's not far from Candi Dasa, 1h drive from Tulamben and just in front of Nusa Penida a few miles off the coast.. hence you can easily get around, besides that it's located in a small village, and not that far from Bai topside attractions, not like Tulamben which is quite dead once dive time is finished.
Tulamben and Amed shoudl be dived early morning when the Kuta/sanur divers are still on the road, you'll see them kitting up on the beach when you're out of your dive.. then it will be time to have lunch in Candi Dasa for instance and dive Gili Tepekong in the afternoon, few divers go there because it's an advanced dive... and you could spend your week like this, just make sure you don't deal with a "money driven only" dive company.
As for the time you could spend on the dive sites : you could stay a month just diving 3 times a day in Bali, tere are lots of intersting areas, all of them providing different kind of diving. The diving is usally split between the following areas : Menjangan, Amed/Tulamben, Candi dasa/Padang Bai and Nusa Penida. (Forget about Sanur diving).
Each area would deserve five days.
Sipadan: I must admit, in addition to the world class diving, the Kapalai Beach Resort looks great. It is a bit more expensive then Bali (which seems cheaper than many other places).
Mmmh... well, I wouldn't care staying on Kapalai which is just a sandbar... I have stayed twice on Sipadan island before it closed and also stayed twice on Mabul, probably this is a reason why my Sipadan stay made me appreciate the place more than Travelnsj does (I think I dived quite a LOT of places too but Sipadan comes high on my list).
Unfortunately Sipadan island is closed for sleeping now. I would rather recommend Borneo Divers, SWV or SMART on Mabul, with a less isolated feel than Kapalai. Not much more to do, but at least there's a small village behind where I used to meet the people and take photos.
... Nusa Penida is good for Mantas and Mola mola too.. again fierce curents... 
