Check out the graphics. All of the characters, what with their empty eyes and vacant smiles, look like they jumped out of a Cathy comic strip. The Game Over screen, which shows the characters as angels and is only in this version, looks particularly ludicrous. The box cover shows them all as super deformed dwarves, although at least there's some cool artwork in the manual. (Images from here.)
There's no scrolling whatsoever - everything moves screen by screen. The longer backgrounds are either split up into multiple screens or condensed into one. Various background details are missing, although it has the nude statue that was taken out the NES version. Outside of a few original tunes here and there (and an especially aggravating pause ditty), most of the game is played without music, much like the PC versions. The only noises are the annoying footstep noise when your character shuffles from place to place.
The FC version also pares down the interface a bit by removing some the extraneous verbs, like Fix and Unlock. The NES version did the same thing, but made a very welcome improvement - whenever you highlight an object you can interact with, its name pops up at the bottom of the screen. None of the other versions have this exact function, but the PC versions have an extra command called What Is that works the same way. This command is completely missing from the FC version, which makes fumbling around in the dark a huge pain in the ass, because you basically just need to click everywhere. I found this Japanese review which expressed frustration at that one hilarious part where you can accidentally blow up the whole house while looking for the electricity breaker when the lights go out.
This same page brings up something I hadn't thought of, though. The first puzzle in the game is to get through the front door, which is, of course, locked. The solution is a well known cliche - just check under the doormat. But then it dawned on me that this cliche might not be well known outside the English speaking realm, and with the difficulty in finding objects to interact with, it's possible that Japanese players might just give up before they even start. It's interesting how this is the sort of puzzle that might be more difficult due to cultural divides. There are other bits of localization that make the FC version more palatable - the dime becomes a 100 yen coin, and the Three Guys Who Publish Anything apparently have an address in Tokyo. There's even a Japanese style mailbox in the first screen, which I'm not entirely sure makes sense, because there's a regular mailbox in front of the porch two screens over. Huh.
The worst part, though are the passwords. The NES version was kind enough to include a battery. Japanese gamers had to deal with 104 character passwords, officially making them the longest of any game on the system, or perhaps, ever.