I remember this game too! The line action cut scenes were really creepy as a kid. I distinctly remember the hands trying to press through the painting and the ghost luring you deeper into the maze. My dad and I got stuck at the one Othello style puzzle with the amoebas. We went out and bought a guide to get past it, only to learn that the author of the guide couldn’t solve it either.

I’ll grant you the first point, the whole game is centered on space travel simulation, but it’s also the only game I’ve seen that handles what you’re describing. You definitely need to consider atmospheric density though. Managing your speed, angle of attack, and parachutes to avoid overheating is one of the major skills you learn while playing. Some are Earth like (Kerbin), other are thinner (Moho), and some are surrounded in an atmosphere so thick that it makes any return mission a huge achievement (Eve).

Kerbal Space Program?