There are two sides to the design and efficiency coin. As a rule of thumb, more modern motors would have better characteristics due to general improvements in manufacturing (machining tolerances are smaller, for instance), and engineering. Liquid-cooled motors are more efficient, as a rule, than air-cooled, and so forth. However, there are also other considerations.
For instance, I have a 250 cc standard motorcycle (Suzuki TU250X). It uses the same basic engine that Suzuki used on its small DR dual-sports, GN standards, and GZ cruisers since early 80s. However, for the new fuel-injected version that Suzuki introduced in the last few years, the newly re-designed top end (cylinder and head) caused it to make less horse-power than earlier carburetted versions (16 v. 20). Why so?
There are multiple factors for such re-design. First of all, the amount of valves were reduced from four to two. Obviously, it would reduce power, because the more, and the bigger the valves, the more air-fuel mixture can be brought in and out. However, the less valves means less maintenance. And for a commuter motorcycle, fuel economy was more important than sheer power.
Design of the valve openings and cam shaft was also rethought to produce more useful power band for this motorcycle. Having high theoretical horsepower does not mean that that power is readily available. Small sport-bikes and sport-like bikes like Duke, CBR250R or Ninja 250 capable of a lot more horsepower (25‒27 in stock form), however that horsepower is available at high RMP (8000‒10 000 or thereabouts), and in regular street riding it is never achieved, unless some one races by overreving the motor on lower gears. TU250X engine is designed to give mild and more even power band, that does not peak as high, but allows more useful power and torque at lower RPM one would use most often in regular urban traffic. As a result, this bike would not win any races and it takes awhile to get up to high speed (though people pushed it past 135 km/h (85 mph) while drafting), but it is a very capable commuter and easily allows over 200 kg of useful load (rider, passenger, and some gear).
Likewise, Bullet 350 affected by two of these factors: it has very old engine that harkens from 1950s, and it is a standard motorcycle workhorse that is designed for commuting, and not racing. Even the brand new RE 500 cc unit-construction engine with EFI is not that powerful for the same reason.