You are focusing on "OMG! Epic monsters!" right away. That's a bad practice.
Questions:
What level characters are you intending to let your players be?
What is the purpose of their adventure?
Do you intend to have them work cooperatively or do you intend to allow them to squabble?
Who is the villain, and what does he do? (and or, who or what is the antagonist. Your setting does not create one.)
What modifications on normal pathfinder rules do you have in mind, if any?
How long do you intend for your campaign to last?
What starting equipment do you intend to permit the characters to have, and--
what kinds of equipment drops do you intend to have available for your players?
I have only played Pathfinder once, and it was a pre-made sample campaign. It was enjoyable, more or less, but was very short. It had pre-rolled characters to expedite getting started.
To do this properly, you first have to make the high level concept, (Group does X to defeat Y, -- big picture wise) then focus on the places and things they need to go and do to accomplish that, then think about how you want the party to grow and develop along that road. There needs to be side roads, red herrings, and other things involved to make the campaign interesting. Try not to put the game "On rails". Encourage plot progression by making sticking around in early areas get boring, etc, but let there be SOME reward for looking around and exploring.
Your campaign scope seems to create a world where high power humanoids are commonplace, do you intend to introduce some dark elements, like what would actually happen in a world where supermen actually exist alongside those without superpowers? Do you intend to introduce the plot equivalent of kryptonite to help balance this dichotomy in social order? Etc.
It is important to keep in mind what is necessary for good narrative. You are looking for a world that is 'Freely explorable', so I suggest a "non-linear narrative structure", which has a starting point, and keeps track of certain variables to modify the global outcome of the narrative based on the reader (player) choices. You still need to come up with the overall PLOT.
Story plots follow some basic rules, which can help you run a better game. Those rules basically revolve around a starting condition story scape, a conflict of some kind leading to a climactic event (your epic boss, whatever), and then a winding down story arc. Your current world design does not paint a plot-- it just paints a setting FOR a plot. A good campaign has more than just setting, it has a plot-- that's why I keep harping over who your antagonist is, and what his/her/its motives are. It does not have to be a poorly designed tropism type bad guy-- it can just be somebody stupid doing something stupid, that endangers the world in a very serious way. (say, a weak demigod scientist/mage doing experiments on demigods, creating a disease (on accident) that affects them in some abysmal way for instance-- which in turn, may be able to infect gods themselves due to shared genetic heritage) There are all kinds of ways to create the source of conflict required for a plot. Think about what kind of conflict you want your world to experience. There has to be some point of contention for there to be story and narrative. Invent one.
(here are some ideas for sources of conflict within/between your groups-)
1) The HeroFactory has a social problem; Their population has genuine supermen in it, alongside a population of ordinary, weak, humanoids. Supermen aren't guaranteed to be benevolent! There are going to be evil/crooked/malign supermen in the popluation. (EG, psychopath supermen) How does the population deal with its criminals, what tools does it employ to deal with them, and what are the implications of those tools and methods? Does the "normal" population employ magical prosthetic devices to operate on the same level as the supermen, or do the supermen have to undergo some kind of depowering to be in harmony with their less powerful kin? Is there ramant class warfare between the supermen and the weaker humanoids? How does this dynamic work, and what kinds of consequences does it have? ALSO-- Greek heroes needed to go prove themselves in order to be proper heros. In a setting where there are lots of OP humanoids, they cant do that-- this means, culture wise, (using your chosen archetypes), the heros need to be itinerant, and go outside their little hero factory setting to go do great things to earn renown. How do the other factions respond to having supermen constantly barging in, meddling with their business?
2) The underworld stewards have a social problem too: The more orthodox of their religious faith would consider the raising of the undead a profane act, since walking dead ARE NOT RESTFUL DEAD. Throw in some of 1) above (itinerant heros showing up, causing trouble), and you can have some serious shit going on there, as the heros either take sides with the necromantic power wielding reformists, or the necromancy abstaining orthodoxy.
3) The stewards of the dead shouldn't have issue with WHERE the dead they care for come from-- are there any political affiliations with the destruction god follower group you describe? That group would create absurd numbers of corpses, and the meddling affairs of heros would be especially dangerous to their status quo (preventing the genocidal sacrifice will bring about an apocholypse, etc.) Do the destruction gods find the supermen to be especially delicious? If so-- are there any plans by this group to sack and burn the hero factory? What rules do they have concerning demonology in public, etc.
4) What structures do the druidic groups you mention adhere to? What definitions of "nature" do they ascribe as being ideal? What views do they have on the boot knocking gods of the hero-factory upsetting the natural development of normal humanoids through cross-breeding? What views do they have about spending resources to sustain monuments to the dead? What views do they have about the destruction god's abandonment of their proper cycle? Etc---
These groups have potential for natural animosities, based on their assigned tropes-- that's good, we have a powder keg ready to get lit. But what is the catalyst of the plot?
Idea for a plot catalyst:
The herofactory solves its social problem "both ways'-- it creates powerful magical devices intended for use by normal humanoids, AND it uses techniques to de-power dangerous criminal supermen so that they can be properly incarcerated without incurring huge expense on the social coffers. However, this creates animosity with the more destruction aligned supermen, who naturally find this setting unpalatable-- they seek to prove their obvious superiority through their obviously greater might and powers. We only need ONE such individual. Given that the cultists following the gods of destruction and rebirth revere gods that are openly destructive and or demanding, this is a ready made group of psychophants ready to stroke the egos of such vain supermen. Naturally, they will be drawn to take up residence there. Being the offspring of gods and humanoids (and or, 2nd, 3rd, or 4th gen offspring between hybrids) they will have godlike powers, and may fall anywhere in the spectrum between "slightly more magical than mundane humanoids" to "Very nearly godlike themselves", depending on how the subsequent hybrid pairings went off. Culturally, they are not adverse to knocking boots with gods or other supernatural beings. The gods of destruction and rebirth have not really been knocking boots with their own followers, but would they consider that action with such a psychopathic high-powered demigod, taking up residence in their territory? We will say that at least one of their number thinks this is an acceptable solution, since having a powerful destruction aligned demigod helps "assure" bountiful sacrifices-- and arrangements are made. This makes the psychopath demigod happy-- he/she gets a population to ritually abuse and who faun all over him/her, AND the actual god of destruction for that region gets to reap the blood spilled by his/her psychopathy. Fast forward a few years/centuries, and you have some new hybrids with this new god and the demigod-- who return to the hero factory. They would represent a very dangerous element to their population, since the powers of these new demigods would favor destruction and rebirth, per their heritage, and not creation. Throw in the social justice system's forced depowering of criminal elements in their population, and you can get some god-on-god angst going on. (you did WHAT to my kids!?-- etc.)
The devices created by the herofactory to depower dangerous criminal supermen for safe incarceration could also be used as god killers. Depower a god sufficiently that it is no longer omnipotent-- and then kill it using conventional means. A necessity for one culture becomes a dire threat to another. WHoo!!!
The devices created by the herofactory to empower normal humanoids goes against the natural order for humanoids, which gets the druidic sects involved. May consider the hybrid offspring to be unnatural, and needing to be purged-- could very well be a very radical sect in this setting!
So-- we could say that we have a psychopathic demigod who settled into the destruction gods domain, seeking political assylum due to what he/she considers ideological pursecution because of the ideals of harmony and cooperation required for the herofactory social order to not be dystopian horror. They settle in, make alliances, knock boots with real destruction gods, and make hyper-destructive 7/8 god (or something like that) offspring that are stomping around the world. Some of those go back to the hero factory to go visit grandma, or whatever. This causes serious problems there, and some of them get depowered for their bad behavior. This causes animosity in the celestial domain, which causes all kinds of shit to happen-- Hero factory is under attack by the gods of destruction, new things are being created by the creation gods to counter the destruction, and groups opposed to the meddling seize the opportunity to end said meddling using the very tools of the meddlers against them.
BOOM-- major plot conflict ready to drop players into.