1.) Creating talent trees usually starts once a hero's base kit is in a more finalized state. The kit is working together nicely, the abilities all have cool uses and shine in different situations, and the hero is feeling fun to play as and against. At this point we can start looking at adding talents to accentuate their abilities. Usually while we're in the process of working on the base kit, we'll have ideas of what a cool talent would be. Sometimes we have a base kit ability that might be a bit too complicated, so we cut out something and reserve it for a talent idea. Other times, we just have a ton of ideas for a hero and since they all can't fit on the base kit, they ultimately become talents. Eventually we start testing the hero with their talents. We focus on each talent individually and on talent builds. We try to make sure the talents are fun to play with and effective on their own as well as when combined with other talents. Players love discovering new synergies and builds and sometimes even we're surprised by what kind of playstyles become the dominant way to play the hero.
2.) We run into a lot of problems when we put different types of themed talents on the same tier. A good example of this was early on in the Heroes alpha and beta days when Illidan and Tychus both had a suite of survivability talents scattered throughout their tree. The primary way to play these damage dealing heroes was to pick all of the survivability talents rather than the talents that increase their damage. No matter how much we buffed their damage talents, players still felt safer and more effective when using the survivability builds. So instead of just nerfing the survivability talents into the ground, we thought it would make more sense if we put them together, changed their use cases, and let players pick between them. It isn't a perfect solution, but as we've developed more heroes we've become better at finding situations to combine talent themes. Orphea has a lot of tiers that offer both survivability and damage on the same tier, such as at level 7 where she can pick Ravenous Hunger (damage and sustain), Insatiable (pure damage) or Mind Devourer (more CC and damage). Li-Ming also has a lot of tiers that offer different choices -- at level 1 she has mana options alongside damage and survivability options (Power Hungry vs Force Armor). At level 13, Illusionist vs Glass Cannon offers another interesting choice and at 16 she has 3 damage options alongside a pure survivability option (Diamond Skin). In many cases, the type of "build" that you're using may define which talent you end up picking. At the end of the day, what matters most is that players have a wide range of choices and feel effective no matter what build they end up using and that they also feel smart for picking the talents that best suit the game they're in, the team composition they are playing alongside, and the enemy composition they are playing against. When those three concepts don't align, that's typically when you'll see a hero get looked at for a talent update or rework.
3.) We feel the same way about D.Va. We're looking at making some changes to her in the future but don't have anything concrete to announce at the moment.