I think it's a difficult one to actually say who is more reliable. There are such a huge number of factors involved, most of which we're not even aware.
First up, you need to look at the range of Intamin rides compared to B&M. The Intamin catalogue is huge, and they do some very specific modifications for parks. Also, rides like Ka put both the trains and launch systems under a lot of strain. You could argue that "Intamin shouldn't make rides that can't take the strain", but they're delivering to the customer what they're asked.
Next you need to look at components. This is something most people don't think about. The control panels, sensors, motors, buttons, pistons, wires, etc. aren't (usually) made by the coaster manufacturer. Those components are all sub-contracted and installed by third party electricians/engineers. Obviously, If Intamin buy from "Cheap as chips control microprocessors Ltd." rather than "High quality control components (to the Queen) Ltd." and the stuff constantly fails, then Intamin should source from the better supplier. However, sometimes you won't find out how good or bad a component is until it's well into its working life.
Now, this is massively complex to be honest. The manufacturer will work with the component suppliers to produce the control systems, etc. They will provide the components and instructions to the park. They may also provide the engineers to install it, or they may use the component suppliers, or the park may use their engineers. It really depends on the park and the ride.
Once the ride has been signed off, it's up to the park to maintain the ride. So here's point three, running on from the above. Are the park maintaining the ride according to the letter of the manufacturers instructions? Are they using original components, or sourcing them independently (a 2.5Ma Type B solenoid from company A is the same product as one sold by company B after all). To bring costs down, both manufacturers and parks will use commonly available components and it may simply be cost cutting by one or the other that causes breakdowns.
B&M do have breakdown issues. Air is dreadful for instance. This kind of proves point 1 up above, B&M running their prototype ride suffers a lot even today. Bugs in Air have been well ironed out by the time you get to Manta. By doing rinse and repeat rides, B&M can guarantee the quality of their ride designs (in terms of systems) and components. By pushing boundaries and having a diverse ride set, Intamin are more prone to "teething issues".
The sheer number of Intamin rides too makes it more likely you'll find an errant Intamin. Hersheypark will have three Intamins next year and one B&M. Guaranteed you will find that it's three times more likely an Intamin will be broken than the B&M
At Alton, it's more likely you'll find a broken B&M
Finally, I get the impression Intamin are actually quite cheap. B&M like to sell themselves as a Mercedes of Coaster Manufacturers, Intamin are more the Fords. With cheap price comes cheap reliability (you offset this with the ability Intamin have to produce a coaster to your needs).