Traveling through time isn't really that difficult in a "Man I keep dying" sort of sense.
The whole thing is instead just tedious as hell. There are so many steps involved in time traveling and creating good futures that it takes a 3 minute level and it can make it a 8 or 10 minute level.
It's worse than hunting for a needle in a haystack, because when you finish with one haystack there's another one with the next needle in it, and another one after that. Pull up a chair and grind it out. There are no hints. Not really any direction. You just have to wander around enough until you find what you're looking for.
In some cases, like Wacky Workbench, the game actually tries to prevent you from creating a good future by hiding shit in illogical places that go against all practical game design conventions. In literally every other Sonic game, including later Sonic CD levels, you are taught what "crushers" are and that being crushed will instantly kill you and Wacky fuckin' Workbench takes that idea and goes, "Naw, letting yourself get crushed is the only way to get to the robot teleporter."
Go eat a dick, Wacky Workbench. Nobody likes you. Shit like this is why you weren't invited to the Christmas Party with all the other Sonic levels. Even Wing Fortress was invited, and nobody likes Wing Fortress. But you weren't.
Other complaints regarding Sonic CD's difficulty are unrelated to time travel for the most part. Dark10x put it better when he said it was more annoying than anything else; The game frequently puts enemies directly on the path the player is running on, meaning that unless you have the level memorized you're most likely going to run straight in to them.
Worse still, there's multiple places in Tidal Tempest where the flying wasp enemies are placed directly over the mouth of a chasm with springs at the bottom, so when you get sprung up there's a pretty good chance you'll collide with them when you're completely defenseless. That's not me being hyperbolic or theoretical; that's actually happened to me on multiple occasions. Everything seems timed so that the wasp badnik will be in precisely the correct position to collide with Sonic.
This gets even worse in later levels, when they start making springs travel back and forth on wheels and expect you to spring up a narrow shaft... that's surrounded by beds of spikes on the ceiling, so unless you thread the needle just perfectly you're going to take damage. No skill in avoiding those traps, only the foresight of memorization.
Quartz Quadrant is a different beast altogether; in a game that demands you frequently take things slow and carefully (as to not accidentally waste time travel energy before you can find a place with enough space for teleportation), they introduce rocks that drop from the ceiling and the only way to avoid them is to be running at full tilt. On top of that are conveyor belts which will severely impede Sonic's speed even if he is running full tilt.
Going back to Wacky Workbench, ignoring the whole "crushers that don't kill you, even though there are crushers in other parts of the game that do" logical fallacy, you have enemies that are basically 100% hidden until they pop out of the ceiling and hurt you.
"Memorization" is not "thinking". It is trial and error. While there's nothing wrong with a little trial and error in small, metered doses, Sonic CD uses it in anything but moderation. But, hey, to a certain degree, that's Sonic. It's a trait that became a pretty significant part of later Sonic games - especially the Sonic Advance and Sonic Rush games.
You just seem to be in denial of Sonic CD's flaws, SonicMegaDrive.
