There were plenty of good gameplay loops, they just didn't get enough time and development. Spore's biggest shortcoming, in my opinion, is that there's not enough of it.
The creature stage is interesting and fun, partially because it lasts long and there's an exploration element. Then you get to the tribal stage and the second tribal stage but with cars and honestly I kind of just rush through that. Then you get to the end game which is the most interesting (but least customisable) part.
The building blocks for two RTSes are there, but they've been dumbed down so far that there's no fun to be had. With a tech tree and bigger tribes, I think a minor Age of Empires stage could be great. The city stage would have the same benefits, but I can imagine a civ style game portraying the technological and cultural progress from the bronze age to the space age would be a nice intermediate. Instead of your evolutionary tree picking one or two arbitrary flags in each stage, you could keep the tech tree going for much longer. Show me how I got that teraforming equipment, don't just teleport it into the store because I traveled a thousand spots!
The end game could do more. Perhaps a Stellaris style unit distant unit control mechanic would allow for a more realistic galactic simulator, with different ships of your empire whizzing around while you go on your space adventure.
I have a feeling that if the game were developed by a Paradox or a Firaxis, the later stages would be a lot better.
It would be fun if Paradox were to set up a system where you can automatically launch the next game, all the way from Rome Total War through Hearts of Iron, and maybe jump to Stellaris from there. I know converters exist but it's not a perfectly clean process with fan projects needed for some steps.