i just had an epiphany the other day, a game heavily influenced by SPORE but with the following changes:
1. Adaptations over time and based on certain actions: of course a good part of the game was about creativity and building whatever cool alien you wanted to make but in terms of progression you never felt like it was proper evolution, in this case instead of unlocking parts and things like that by doing random shit you would have some kind of "Adaptations Tree" from which you would choose which things to evolve on your creature. these adaptations would be obtained by doing certain actions like for example jumping and climbing may lead to gliding adaptations then maybe later lead to flying adaptations. by the time the player gets to the Society Stage this adaptation system transforms into a technology tree from which you advance the civilization and so on. kinda like Tech Trees in any RTS game.
2. Actual Niches: the Herbivore/Carnivore/Omnivore triad was cool as a testing ground but i think there were some other things that could have been added as alternatives. Detritivores that fed on decayed matter, scavengers that fed on rotten carcasses, parasites, chemovores and perhaps photosynthetic creatures could have been easily added into the game. Niches would also mean different sources of nourishment for the player so this would tie with Adaptations in order to ensure the player has to put actual thinking on how it wants to evolve its creature, you wouldnt just swap from Carnivore to Herbivore by just changing the mouth on the first hatch, perhaps these adaptations would be inversely proportional so if you wanted your carnivore to convert into a herbivore to survive during a random event you would have to slowly decrease your progress in carnivore adaptations until you could jump into omnivore then keep going with the vegetation diet until herbivore adaptations started to be unlocked.
3. Better spacing between stages: the original game was fine as it was, i would have liked it to be like in the 2003-2005 demos but the final product was just as good and could have been even better if properly handled via DLC and stuff like that. the time between stages was one of many issues with the game, your species was supposed to reach space eventually but somethings it felt very rushed, changing the difficulty would have done nothing to alleviate this because from the start there wasnt enough time sink added to the stages. in this game the stages would follow the same pattern as in SPORE but with more defining transitions that could also unlock extra functionalities for the next one.
-Microbe Stage -> longer than Cell, it starts with the player microbe surviving and adapting after arriving into the planet, the first milestone comes from attaching yourself to other microbes to form a colony, the second milestone comes when your microbial colony has grown big enough and obtains enough genetical material to unlock multicellularity. this stage features a different set of adaptations compared to SPORE with things like chemosynthetis, photosynthesis, photoreceptors (as replacement for the googly eyes), etc..
-Creature Stage -> this one includes the acuatic stage which is the starting part, the first milestone is getting into land, the second is unlocking advanced intelligence. the progression wouldnt be forced so for example your creature could return to the ocean over a few million years, albeit aquatic civilization would be tricky to develop.
-Civilization Stage -> this one makes a transition between Tribal and Civilization stage in the original SPORE, the first milestone is passing from a simple tribe into constructing the first city states in the planet, the second milestone consists into producing the first steam engine and thus enablign the construction of mechanical vehicles as replacement to mounted gatherers. the final milestone is taking over the whole planet. the adaptations obtained during creature would have had an impact on what resources you need the most to survive as a society, but in this stage is where the technology tree comes up and you have to flesh out the social aspects of your species which have some ties to some creature adaptations like "pack hunting", "herding", etc...
-Space Stage -> so, your civilization was able to cover the whole planet (and exterminate or include any other sentient race that arose in the world) the Space stage starts with the player sending its first spaceship to explore the star system, the first milestone consists into developing the technology to travel and colonize in other stars, the second milestone consists into developing warp travel for exploring more distant parts of the galaxy, the final milestone ends in ascending the race to a superior state (achieving godhood). all of this while dealing with 4X style elements like other empires harassing you or seeking aid, managing your colonies, the different alien races you have under your fold. kinda like Stellaris, but you still have some sort of "heroe" or "captain" unit to go around and get extra missions from the aliens.
4. Different Starts and Endings: i think the game could have felt more interesting if you could decide on which conditions to start the game. things like harsher environments or events rapidly obliguing the player to adapt in order to survivea. this would extend in all stages probably, and could include different ends to the player species like nuclear war, an asteroid impact, being swallowed by a cosmic entity, etc...
after finishing the last milestone you would unlock everything in the editors, including extra stuff like flora and planets. to be honest, if your think about it we're on an age where we could replicate how did this game worked in an engine like Unity, there's still probably some things that only the people at Maxis could do but everything from planet generation to dynamic meshes for the creatures and vehicles could be done in the most recent engines avaliable. and there would probably be space to improve on what the game couldnt, the only hard part to implement i think is doing something similar to the Sporepedia.