I kind of like these suggestions, in a perfect world, maybe Jeff could implement these and other suggestions and GeneForge would be world famous.
Yeah, melee sucks, everyone knows that. The first three GeneForge games were made roughly around the time of the first three Avernum games, and borrowed on the combat. So it's to be expected that the melee is kind of boring. I would say the laziest solution is to implement the melee abilities from Avernum and call it a day. I like where your going by making multi-attack dependent on melee and improving crit on missiles. Melee builds are usually durable and they can survive long enough for multi-attack procs to whittle enemies down. Whereas Ranged builds tend to be fragile and the crit will help them burst enemies before they can touch them.
The idea of a third "perfected" tier is kind of interesting, though it doesn't really follow with GeneForge's story, I can see it being implemented in the game. It's been explained that new creation models are found by bombarding pre-existing organisms with magical radiation, in hopes of finding something useful. Even the rebels do this, despite knowing how genes work. So finding a "perfect" model of a creation is really unlikely.
The Bad, Good, and Golden were pretty cool to read. The strongest point of each ending, is that they feel like sub-factions within the factions themselves. The rebel endings are the most obvious examples, where the rebels have broken into three different branches: Drakons, Humans and Serviles, but each have their own take on the rebel ideology.
Some of the endings sound weak or completely boring. Take for example, Alwan's bad ending, where you have this massive melee fight that...
With GeneForge's combat engine, that would be unbearable. I suspect that you're familiar with the area south of Perikalia in GeneForge 5, where rogues invade the city. That was the WORST area for me. I'd rather grind through the entire game on Torment with nothing but ornks, because there were so many NPCs and enemies on that map that I had to wait 1 minute between each turn. I got so bored that I just hid from the rogues, until the guards or rogues were slaughtered.
Nevertheless, if GeneForge had this elaborate of a story, I would have no doubt that it would be compared to something like PlaneScape: Torment.