There really are no shortcomings to the MEP-002a / MEP-003a design that make them in need of any updating, they do however have a few common issues that are not critical to their operation.
1, Some argue that the voltage regulation system is overly complex, it is certainly esoteric compared to modern commercial AVR's.To put it in simple terms most commercial AVR's work by boosting the excitation field to the desired level, whereby a complete failure of the AVR circuit board generally results in no voltage being produced by the generator, by contrast the AVR's on the MEP-002a / MEP-003a work by dampening a full voltage output which is produced by a type of transformer, meaning its most common failure mode causes the voltage to go high. (about 150VAC instead of 120VAC). Having said that the standard AVR circuit is well built, and fairly reliable, it is also economically repairable with the most common failure component a $5 transistor that can be replaced by anyone with basic soldering skills. (3 legs to solder and one screw to remove). Personally I see no benefit in replacing a working or economically repairable AVR system with a commercial drop in product.
2, The other most common problems with these generators when they are in running condition has to do with the instrumentation, this is due to multiple issues, the gauges themselves tend to fail or go out of calibration due to vibration and moisture, and the frequency transducer that drives the frequency meter is failure prone due to aging components. Having said that none of these gauges are critical to the operation of the unit, some people choose to retrofit modern digital gauges to their generators, but this usually involves some metal work on the part of the front panel holes, etc. as original style gauges can by hard to locate and prohibitively expensive. It is always a good idea to double check the panel meter accuracy with a known good meter, the cheap ($20 from Amazon, etc) Kill-A-Watt P4400 is nearly ideal for this.
3, I do not mention injector pumps here as failure of those are often attributed to long term improper storage and are therefore not relevant to the topic at hand.
Overall it is rare to see failures in these generators once people have them up and running, and when we do it is not any one specific component, but instead random failure like you might find with any mechanical device.
Ike
p.s. I might add DC charging regulators as a age / wear prone component, while I probably would not replace a working one, it might be smart to have a spare on hand, much like having a spare or two of those $5 transistors.