The Foot Clan's ambush of the Turtles and April at 2nd Time Around is escalated when one of the Foot mooks swings a Bisento axe and cuts through a power line, ELECTROCUTING HIMSELF, as well as starting a fire. Furthermore, the gang (including a gravely injured Raphael,) only makes it out alive due to the intervention of Casey Jones, and pretty much at the last second. We see April and Danny Pennington respectively, both distraught, watching her apartment go up in flames. What we don't see is how (or more appropriately, IF) the dozen or so Foot ninja that were knocked out during the melee ever escaped. You may write this off as "They're henchmen, so who cares?" Well, remember that the bulk of the Foot's recruitment (we never find out how many emigrated with Shredder from Japan) was aimed at TEENAGERS, some appearing as young as 13.
Slightly mitigated in that the Foot seem to recruit on a "milk before meat" approach in the first film: they lure in young teenagers with promises of cigars, skateboards, and other fun, and as the children get older they are taught martial arts and eventually indoctrinated into becoming Foot Soldiers, meaning that the ninjas attacking the Turtles are likely to be at least 18.
The Foot hasn't apparently been active for long enough to train a significant number of young ones anyways. Through the fight, just about any time you can see eyes through the mask, they are Asian-ish, and the Foot members have Asian-style voices (watch enough anime subbed and you can pick up on how their very grunts of pain or effort sound differently). Virtually all of the actual masked fighters are old guard, not recruited teens. At the beginning of the movie, April's report calls this a "recent" crime surge.
More squicky than truly horrific, but April has to spend a lot of time walking ankle deep through drainage water while wearing a short skirt and high heels. Makes her animated counterpart's yellow jumpsuit seem both practical and hygienic.
When the Turtles are returning to the lair from the farm she's actually carrying her shoes, which is somehow both better and worse at the same time.
Casey Jones humiliated Tatsu and seemingly killed Shredder. If the turtles are fearful enough of the Foot not to go back to the sewer, you can bet Casey had a damn good reason to leave town for a little while.
Shredder's fighting technique used during the battle with the turtles at the end of the movie. If you watch his movements you see he is being very conservative. A few quick blows, then stepping back. Never exposing himself by going for a killing blow and letting the turtles come to him instead of running at them. As he is fighting against four other people who are not even half his age, if he were to get winded or badly hurt he could very well be easily overwhelmed.
There's also a possible hint of I Let You Win as you realize that the Foot possibly never meant to actually beat the Turtles, but lull them into overconfidence and lure them to the roof where the Shredder is waiting or just wear them down making them easier to fight.
When they find their home ransacked and Splinter missing. Raphael takes it harder than the others. Though this may be his classic rage breaking on the surface. If we really look into it, he blames himself because he manages to piece together how they may have found their sewer home. Judging by the look on his face he was thinking about the events prior to April meeting the turtles, from the Subway fight to escorting her home.
In that same vein, Michelangelo brushing off Donatello over the concept of Splinter being gone takes on a different meaning when you see him crying the hardest later in the campfire scene. It's most likely that the thought of Splinter being gone was just too much for him to bear, to the point where he didn't even want to discuss it.
The lyrics in Turtle Power which state that Raph is the leader. Sure in all incarnations, Leo is the leader, but the 1990 movie is the version that highlights a strong-yet-subtle emphasis on Leo's inexperience as a leader. Had Steve Barron been re-hired to do TMNT 2 and 3, most likely he would've developed Leo into the Badass Leader that we know him to be. But in this movie, Raph proves he's just as capable a leader as Leo is.
Raph is presented as the most serious and proactive of his brothers, having displayed some Chronic Hero Syndrome throughout the film.
A leader has to be able to make hard decisions. Early on, when Raph rescues April and brings her to their home (blowing their secret existence), his brothers (Leo included) ask him why he would do it - implying that while they would have protected April, they would have just left her unconscious form alone until she woke up. Raph implies that though both sides of the scenario had positives and negatives, his decision ensured that April would be safe.
Raph takes the lead in the battle just before they meet Shredder, chasing the Foot to the rooftops. What's also interesting to note is that Mikey, Donnie and Leo wisecrack a bit in this scene, but not Raph.
Raph, again, shows marks of a great leader in the final battle against Shredder. He's the first to test the waters against Shredder. He also keeps his cool when Shredder taunts them - and Leo of all turtles is the one to fly into a rage. Raph also makes the decision to throw away their weapons in an effort to save Leo - who got pinned down by Shredder.
The fighting in the apartment is frenetic and clumsy. Which makes sense when you realize that the Turtles and the majority of the Foot are young ninjas and this is their first battle.
As the apartment gets more and more crowded, formal ninja weapons (swords, axes, staffs and nunchucks) are discarded and more progress is made with fists and improvised weapons (floor planks, cymbals, bike parts, anything that is a hard object, etc.). Also, mobility is restricted, so the melee degenerates into a brutal brawl as the fight heats up.
And once Casey shows up he helps turn the tide and utterly curbstomps the Foot, successfully holding the line until the Turtles can escape. Casey is older, more experienced, and used to fighting in confined alleys as part of his vigilante activities. He's also a Combat Pragmatist of the highest order (ask Tatsu).
Regarding fights, the movie makes subtle efforts to NOT portray battles as fun and games. All of the fights have suspenseful and intense music. If goofy music is played beforehand, it was just to mislead you into thinking the Turtles stood a chance.
The Shredder threatens to our heroes by telling them that he was going to dine on turtle soup. Sure, it sounds silly, until you think about what that means. He basically said he was going to kill, cook, and eat our heroes.
The first encounter with the Foot Clan is both this and Getting Crap Past the Radar. In the scene, the Turtles are assaulted by people wearing uniforms that they have not met yet. Raphael stabs a mook in the stomach, revealing it's robotic origins. This of course, allows the violence of the show, as only inanimate robots are ever harmed. The horror sets in when you realize that Raphael just stabbed a guy. If it hadn't been a robot...