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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.
As far as songs go, Let Mom Sleep (No Sleep Remix) has become surprisingly popular in mashups despite being the least played song in JSRF.
"Funny Aneurysm" Moment: Teargassing teens, using excessive force for something mostly passive and peaceful, police brutality on an extreme level, all become severely less funny and cartoony when you realize that sort of thing happens with alarming frequency these days.
Rescued from the Scrappy Heap: Yoyo was retooled from a short, chubby, annoying kid who challenged you to a painful race in JSR into a much more likable and attractive character in JSRF.
In JSRF, the Tokyo Undergound Sewage Facility. Interestingly, due to the way the soundtrack is structured in-game, the Sewage Facility is the first level where The Scrappy plays.
Bonus points for one of its final graffiti souls, which requires using the wall-ride move up a narrow vertical passage; the walls must be ridden in sequence (as trying to wall ride the same wall twice in a row doesn't work), the two safety platforms contain no barriers to stop you accidentally falling, getting stuck in a wall corner is very easy and the walls are covered in non-wall-ride-able sections designed to make you fall back to the start.
No "love" for the Skyscraper Distract & Pharaoh Park? Dark color pallete, tons of life-sapping Non-Lethal Bottomless Pits, and very specific series of rails to grind and jumps to make combine into one hellish experience, especially when traveling into the very far reaches.
Hikage Street is full of incredibly boring level design, frequent stops to fight the police, and having to climb up the stairs repeatedly due to all the graffiti being at the top and it being incredibly easy to fall back to the bottom.
Bantam Street in the original game, especially with a hard-to-reach tag that usually ends up to be the last one to be done with barely any time on the clock left.
The Hikage Street Terror Drone is all that but worse. Hard to get in a hit on it, a flow-crushing cutscene in the middle of the battle and an agonizingly long trek back up, plus framerate drops to the bombs going off making it even slower.
They Changed It, Now It Sucks: Initially, a huge chunk of the soundtrack couldn't be licensed again for the Updated Re-release, which caused a lot of this. Fortunately, it has been reduced to two songs, with Sega trying to get the rights to those. Thankfully, leaving aside one song, this was not the case for the HD rerelease.
What Do You Mean, It's Not for Kids?: Many were probably confused by the Teen rating on the game, even through the first few playthroughs...until they listened closely to the lyrics of most of the songs. One of said songs gives you tips on how to give a good blowjob. Another has you hearing the whispered moans of a loving couple, busy in the sack. You also hear LOTS of references to polyamory. Also, the song "Rockin' the Mic" contains constant use of the S-word and N-word. Yeah, seriously. Go listen, it's CRAZY.