I just did some budget diving in Wakatobi last month.
I went to two islands there, Pulau Tomia and Pulau Hoga.
Tomia is where the Wakatobi resort is, but since they're out of my price range I didn't dive with them.
I dived with Tomia Dive Center instead.
AFAIK, TDC is the only dive centre in the area other than Wakatobi resort.
Tomia is an awesome place to dive.
The sheer number of marine life there is amazing.
Barracudas, wrasse, moray, triggerfish, etc.
The sites I dived are mostly walls and some pinnacle / ridge.
There are macro sites too, but we didn't go there because the current is too strong.
For sites in Tomia, check out this link:
Wakatobi Dive Resort - Dive Sites and Descriptions
Now the bad thing with TDC is that they only have 1 divemaster, and he was not in Tomia when I got there.
So I dived with his brother, which is a diver but certainly not a divemaster i.e he didn't have extensive knowledge of the dive sites and he definitely doesn't have "eagle eyes".
Most of the time, it was me who lead the dive and he was basically only there to help me in case something wrong happened.
TDC is really small operation and they don't have a resort or anything.
I slept at a spare room at their dive center, and the neighbouring villagers make dinner for us.
So accomodation wise, it was all pretty basic.
In total I spent 380 USD for 10 dives and 4 days in Tomia.
In Tomia, there's only electricity at night.
They have cellphone signal though, so you can have (slow) internet.
In Hoga, I dived with Tukang Besi Diving.
The dive sites are similar but slightly inferior than Tomia.
They do have better accomodation (still basic) and the food is great.
The divemaster is also better.
Another major plus is you get white sandy beach and a great place just to relax and do nothing.
In Hoga I spent 330 USD for 7 dives and 5 days.
IMO, You'll get a better overall experience in Bunaken, but from a purely diving prespective Tomia / Hoga win hands down.
If you don't mind roughing it a bit, I'd definitely recommend them.
Lembeh is different than Bunaken / Tomia / Hoga, it's such a unique place, especially if you love macro.
They don't cal call it the critter capital for nothing.
For TDC, contact Yudi +62 856 5656 1560.
You can try emailing them (contact_us@tomiadivecentre.com) but the internet connection there is bad, so it might take a week or two for them to reply.
Tukang Besi Diving is here (
http://www.tukangbesidiving.com/) or talk to Geertje at +62 815 2466 5350