Burning Bridges, for Eve or Jool to be properly "simulated" and feel alien (and also challenging) you would need:
- parts with different atmospheric pressure tolerance, explode/fail when there's too much pressure.
- better part temperature/overheating model and ways to cool parts/radiate heat.
- weather, wind in particular but also lightning, fog, clouds.
- radiation.
I think the first one could be done using the tweakables feature in the editor rather than by making a billion variants of everything. Just like you can set a tank to be half-full in the VAB now, you could increase the base pressure-resistance of parts at the cost of both more money and vehicle mass. If proper ocean simulation was also added this would also be useful. Although I think implementing drilling holes in ice of a Europa equivalent could be a problem.
The second one is a no-brainer, the basic mechanics are already there, system just needs some work.
As for the third one, wind is just a random force dependent on atmo pressure and own velocity. Not that hard to do I think. I'm not sure how to implement lightning without it feeling like a random "lol you're fucked bro" mechanic with simplistic counterplay. Lightning rods? How to make using them interesting than slap one on not to fry your ship? Fog is pretty easy to explain, but apparently unity gave them performance issues when they tried implementing it last time. Rain without a complex flooding/liquid system makes no sense from a simulation perspective, only as visual fluff but it would be a nice touch.
Radiation is basically fixed with either more shielding or hardening so it is a bit similar to pressure, but I think that apart from crew modules, probe cores, SAS and science parts most parts don't need to have a rad resistance stat. Just the ones housing lifeforms or electronics. For electronics the issue would be mostly cost rather than mass, adding more incentive to not risk kerbals.
Environments are really lacking at the moment which is why as you noted it seems like there's basically just two of celestial body archetypes now. Proper weather condition would go a long way into making things feel different. Also look at rovers, as long as there's no liquid around it matters little where you drive them. There's the difference in gravity but what about surfaces? Why not tweakable rover wheels with spikes for better grip on ice? Maybe wheels that work better in the dust of Duna. Why not have threads? More enviromental hazards? Hell, think of floating ice bergs on Laythe's poles, streams and puddles of alien liquid on eve. What about risk of equipment freezing if you don't have enough heating?
The thing is though, how hardcore and deep do the devs want to go? That's the only thing I worry about at times, especially considering their reluctance to add re-entry heat or life support management. I *think* that with difficulty modes added we may see some of those more sim features, but I'm not sure how many.