In short, there are no "best dice" to use. Different dice and different methods of using those dice, give different results. Depending on what you want out of your game system, different options will do better for you. Replace 3d6 with 2d4+1d10 and you get the same range and average value, but extremes become somewhat more likely. Percentile dice are great if you want to have a fine-grain detail. If you just end up assigning all bonuses and penalties in chunks of +/-5, then you might as well use d20. Whatever you choose based on your initial vision, be prepared to change it as you actually try things out and make adjustments.