It's the pulley's job to dampen, not the flywheel. The weight of the flywheel does not affect dampening or wear of the bearings unless something is wrong with the setup.
Most lightweight flywheels are balanced, so they do not ADD any negative vibrations or do anything improper to create excess bearing wear, it just helps ensure neutrality on one end of the crank. The factory pulley is balanced, or at least more well balanced than most aftermarket items. The lure of aftermarket items is in the idea of increased power. But, you must ask yourself something. Don't you think the engineers at Honda who CAME UP with each engine knew a few more things about it's power capabilities and health\reliability when they made them? Aftermarket companies are rarely ever backed by any actual mechanical engineering or otherwise valid experience to add credential to their claims of their products making power. They build items based on engineering concepts, whereas OE components where designed specifically for their application with great detail and prior thought. The people at AEM, DC, Apexi, UR or any other company GENERALLY are not more intelligent than the people who designed the engines in the first place that these people make products for. They simply do not know as much as the people who set these engines up specifically one way for a reason. This is why many aftermarket parts either provide only marginal performance gains, or offer an increased likelihood of lost performance in another aspect, or lesser efficiency in engine function leading to premature wear or failure.
your local machine shop knows more than you about your engine and what to do with it. They'll know what it really needs better and see more when they take it apart than you will. Just ask them about what they think for your goals, break the various prices down for you, give them your budget, and let them make the decisions. If I brought my car to you because I was ignorant about it and you weren't, and knew it needed help, but I told you to crap in the combustion chambers because that's what I thought it needed, you'd roll your eyes because you know it's not what's necessary to do the job (since you do it all the time and know better than I do, hence, you are the professional here not me), but you would do what you were paid to, and then have to defend yourself when I come back angry cause it doesn't run right. stupid customer requests cause a lot of problems, sometimes it really is best to leave it to a pro. Machining's not something you just figure out, it takes training.