These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Epileptic Trees / Everyone Is Jesus in Purgatory: Like its successors, a magnet for these, especially concerning Giygas. The backstory is more implied than spelled out, leaving plenty of room for interpretation. Same thing with most of the setting, like Duncan's Factory.
Heartwarming/Hilarious in Hindsight: Shigesato Itoi was known to smoke a lot. The Crow smoked in the original release, but after the unreleased English version Bowdlerised that, the change was also in MOTHER 1+2. Near the time MOTHER 1+2 was released, Itoi quit smoking.
Goddamned Bats: Plenty of these, too, especially since you can't skip low-level encounters like you can in the sequels.
Jerkass Woobie : Giygas loved Maria very much, but was forced to lead the Earth invasion by his people for vengeance on George for stealing their PSI information. He killed her in attempt to get rid of his deep feelings of love for her, but that doesn't work.
Player Punch: Giygas begs you repeatedly to stop when you fight him and start singing the Lullaby.
Polished Port: The MOTHER 1+ part of MOTHER 1+2 is much more accurate of a port (and even received some updates) than the lower-quality MOTHER 2 side of it was. Despite this, it was MOTHER 2 that was the focus of the game's commercials.
Scrappy Mechanic: The battle system may be the sole reason why this game is less popular than its sequels outside of Japan, as it's just a bad Dragon Quest clone in terms of gameplay. (Remember that the reason Itoi decided to make a video game in the first place is because he played Dragon Quest, so the similarity is inevitable.)
The fact that random NP Cs can give Ninten a cold, which acts like poison and can only be gotten rid of by a trip to the doctor or some Mouthwash (which you can't buy until you reach Snowman.)
Sequel Displacement: Despite being the first Mother game, it's the most obscure. Notice how Ness, Lucas, Porky, and various references to their games are in the Super Smash Bros. series, but all this game gets is some music (most of which are used in all three games, or at least EarthBound) and a few stickers in Brawl.
That One Boss: The game has only a handful of bosses, but the Dragon in Magicant stands out for his powerful normal attacks and devastating PSI. Even with a PSI-Block from Ana, it's still a very challenging fight.
That One Level: Holy-Loly Mountain/Mt. Itoi, to some Duncan Factory due to it's massive size.
Unfortunate Implications: One NPC remarks that the gym teacher beats him and ponders dropping out of school and becoming a thug. This was changed into doing extra push-ups (and preferring sit-ups) in Earth Bound/EarthBound Zero.
Woolseyism: Many of the (Itoi-approved) changes Nintendo of America made in the unreleased American version, including the run button and an epilogue, were added to the game in Mother 1+2, a GBA port of this game and EarthBound.