Budget is relative and we're talking a Raja Ampat trip, but...are you looking at lower budget, mid.-range or higher end boats? All other things being equal, would you pay several hundred bucks for an otherwise similar experience, but a more beautiful boat, a more luxurious vibe, etc...?
One factor of potential interest to some people is the availability of larger tanks. Haven't been there; doing some research on the destination recently, I learned the
Samambaia has some big tanks (15-liter) one can rent; the
Indo Siren has some, also, and no extra charge per my dive travel agent Tim Yeo with Blue Water Dive Travel, but they may switch them around depending on needs (in other words, you might have to give it up if there's a bigger air hog than you onboard, so you might not want to routinely get back on the boat with
too much ending tank pressure). He recommended a minimum 10-night trip, so as to have time to dive south, north and far north Raja Ampat.
Those Phinisi boats are a regional thing in Indonesia, from what I understand; they look beautiful. Some boats (e.g.:
Indo Siren) look to be Phinisi, and some (e.g.:
Raja Ampat Aggressor) do not.
Those of you who've been to Indonesia and tried the Phinisi boats, is that a factor in your preferences? Can you tell us the pro.s & con.s of the two?
Since your thread hasn't picked up much steam yet, I'll shoot a shout out to
@Dan - he's been to that part of the world, and done some live-aboards.