To better help you with your answer I did some searching on the net. I see you posted this say question in several areas. Which I think is a good thing. I did notice a few things. It think the engines are the same HP. Just one person referred to size (cubic inches) and the other referred to HP. Make sure you look at who you are asking what questions. No matter what its hard not to suspect some bias or un-informed responses.
Mastercraft owners will say their boat is best.
Moomba owners will say, just as good as others but no name flashing so the price is lower.
The big thing between companies is the details in the finishing. MC and Moomba use the same engine supplier. I think most to all boats use the same company for control parts. MC might use more stainless or aluminum instead of fiberglass or plastic which makes the cost differ.
I would look at personal preferences. Each boat has lots of life yet. Colors and styling. If low hrs are important, then MC. My 03 Outback only had 85 hrs at 7 yrs old when I purchased and it has been good for me. Or if newer model has your interest, then Moomba.
For me name brand or resale was not an issue. Remember these not investment, they are B.O.A.T.s (bust out another thousand), a hobby, a recreational vehilce. They serve no pratical purpose other than enjoyment.
I would also look at the seller. Which one make me feel more comfortable and confident.
I would look at it more like a GM truck. Do I want a GMC or a Chevy. Both do the same thing with the same engine.
And to note I am Moomba Bias
unless I would ever buy something different.
2003 Outback, Assault EFI, (6) Polk Audio DB651s, JL Audio M6600 amp, JL Audio M1700 amp, JL Audio 10w6v2 subwoofer