Is it better to have less flywheel weight on exercise bikes?
Workout quality is determined by the power output you can sustain through the course of your effort(s), and if the power is lower than it might be because of a lack of crank inertial load, then the training stimulus will be less. 

Keep in mind that the most important adaptations are metabolic, not neural. Changes to pedalling action has not been shown to convert to improved power output, except for the specific situation being trained.

It's common for people to find riding on low inertia trainers (e.g. cheap magnetic resistance units) unable to generate the same power as when riding a high(er) inertia trainer. The crank inertial load doesn't need to be as high as that experienced in typical outdoor riding, just sufficient to avoid that awful draggy sensation.

There are quite a number of published studies about varying crank length and chainring shape. The balance of evidence on these is that on average, such interventions neither harm nor enhance your sustainable or maximal power output.

As a general rule of thumb, if you find using a trainer results in a power output 10+% less than you would ordinarily be capable of, then I'd suggest looking at making changes to your trainer set up. That may or may not include increasing the crank inertial load but often means paying attention to other factors such as having adequate cooling (very important) and use of motivational aids.