Hi, first of all I'll let you know upfront I own a dive business in Kota Kinabalu (it's in my profile). I don't have experience with Dive Operators in Semporna (I've been lucky enough to stay at Resorts near Sipadan). However I can share advice, as a PADI Professional, on areas you should check with the Dive Operators you are considering using in Semporna. All the areas below can be checked with the Dive Operators you are considering by email or online - so can be done in advance of your trip.
Check that the Dive Operators you are condiering are authorised as a Dive Operator with PADI, SSI, SDI (or a recognised Diving Association) - you can ask them if they are an authorised Dive Operator as well as check the web site listing for PADI etc. This hopefully means you'll be guided by qualified Dive Professionals.
Ask them what ratios they use for guided dives i.e. how many certified divers per dive guide. The lower, the better for you. You should also ask for their diving schedule so you can get an idea of the mix of diving you'll get to enjoy.
With diving you generally get what you pay for - so the cheapest isn't always the best. Check that the dive gear is regularly maintained (including cylinders). Check what's included / excluded from your diving trip price - to avoid any surprises.
Generally, ask as many questions as possible via email and go with the Dive Operator who takes the time to answer them (as most Dive Operations welcome customers wanting to know more) and you feel most comfortable with.
Enjoy your diving holiday from Semporna. I'm sure you'll enjoy fantastic diving and have a wonderful time!