I like the concept, but I'm confident that a voting/nomination thread is probably not the best immediate course of action. I feel like these sorts of things need a clear criteria on how you'd judge them. The traditional criteria in HOTY would be uninteresting and boring to see again. Perhaps if you added more subjective and interesting criteria such as historical significance to the scene, completeness and even groundbreaking aspects introduced for the first time in the generation.
I feel like if we kept the voting pole and nomination system with the end results being judged based on current features, we'd basically be dismissing some great and famous hacks created throughout the years. Hacks like ShinyGold, Rijon Adventures, Genesis, and even Quartz to a degree!
From an article like this, I'd rather see your subjective views on the greatest hacks PC has to offer. I'd rather see what hacks influenced the writer's experiences than see something which represents the most popular hacks on PC. Maybe these can be separate articles. I do think that "Top 5 Lists" are extremely popular and definitely will be well received, however the goals and objective of your top 5 list should be based on more than solely popularity among currently active users. Some levels of subjectivity would make sense, because your list can't be absolute anyways :)