I just got back from Sipidan (well, technically Lankayan was the last place I was at), I stayed at Mabul Water Bungalows for my Sipidan diving. Its still under construction, but what they have finished is great. You will have to live with a little bit of construction noise. They will lug the gear from the dockside onto the boat, or you can do it yourself if you're more paranoid about your gear. The dive boats come from SMART, but they have a dock where they pick you up. You're gear is stored about 15 feet from the boat at the top of the stairway for the shore dive entry. The entry point for the short dive at Froggy's lair is easy, and it makes for a great shore dive as well. The rooms are air conditioned, the food was great, and, at least when I booked, it was cheaper than Sipidan Water Village. They give you 2 dives a day at Sipidan, plus one boat dive at Mabul or Kapalai.
www.mabulwaterbungalows.com. I'd go back again. From what I've heard, I just wish I'd gotten out to Sipidan about, oh, 10-15 years ago.