The problem is that you look at the street fighting game genre as a given and take for granted everything built around the SFII formula. Even the things from the first Street Fighter that SFII carries over aren't influencing everything after SFII, only SFII itself is. SNK actually hired every Street Fighter II team member they could to pump out variations on SFII for Neo Geo.
Samurai Spirits has some cool aspects that helped it stand apart from the other early SFII-cash-in games and influenced some other games which also never went full mainstream. But in the overall genre it isn't very original and therefore not really groundbreaking. Weaponlord is a much more groundbreaking weapons-involving fighter.
So how does Samurai Spirits "look nothing like" SFII and other street fighting games? The "weapon system" isn't very unique or complicated, coming after Time Killers. A game when compared to, really highlights SS's typical SFII movement, combos, progression, design, etc.
I'm not going to go full blown into debate mode here concerning everything you have said but I do want to make a few points.
1. Virtua Fighter plays and looks nothing like Street Fighter 1 or 2. There are no fireballs or other imaginary mystical type of attacks involved in the game outside of the magical 10 second 2 story jumps. Otherwise the gameplay mimics realistic hand to hand combat. No dizzies, no blood, etc either. If it draws inspiration from anything, it would be Karate Champ, though maybe 9 years late. Cashing in on the Street Fighter craze? Hardly.
2. Fighting games were popular before Street Fighter 2. They had always been good money makers in the arcade scene, whether it was a standard fare beat'em up like Double Dragon, Final Fight, or Ninja Gaiden, or something along the lines of Violence Fight, Pit Fighter, and Street Smart which were more one on one. Granted, Street Fighter 2 was a hit game and very popular.
If it had not come out though it would have had no impact on SNK's ealier fighting game development, as it was already on course as is prior to SF2's release. SNK already had plans set in motion. After SF2 they built on those plans and expanded them, but as is, they already knew what they had in mind when they developed the system with a 4 button control scheme prior to SF2.
3. Takashi Nishiyama and Hiroshi Matsumoto are the Capcom employees who originally left Capcom to go work for SNK. They did this a bit after working on Street Fighter 1. They had nothing to do with Street Fighter 2, and the development of Fatal Fury was taking place during the development of the Neo Geo MVS/AES, prior to the release of Street Fighter 2. Art of Fighting was developed right after they finished developing Fatal Fury 1, still prior to SF2 becoming a huge hit.
AOF was released in 1992. It wasn't just some 6 month rush job to cash in on SF2. No SNK fighter was, and most every SNK fighter brought far more inovation to the table concerning borrowing from and improving upon the gameplay from SF1 then Street Fighter 2 ever did.
Neither game was rushed out the door to copy nor cash in on SF 2, and neither franchise share the same control scheme or combo system SF2 used, let alone story development (Fatal Fury and AOF's plot are both far more mature themed and more developed as shown during gameplay story scenes).
The only thing they borrow from Street Fighter anything is Street Fighter 1 on the special move motions, which I mean hey, they have that right I suppose, since they were developed by the guys who originally came up with it. Capcom later lost more employees, but supposedly it was due to staff being tired of rehashing SF2 in updates.
4. Pretty much any fighting game developed by SNK after AOF and Fatal Fury 1 tended to avoid copying Street Fighter 2 all together (No comment on Data East or other developers who borrowed from both SNK and Capcom). The few that do directly borrow control schemes from Street Fighter 1, which started the whole light/med/strong attack and special move system are like Fatal Fury 2/Special, and Samurai Showdown 1 and 2 (3-5 came up with new control schemes), and the KOF series.
Street Fighter 2 is just as guilty as any of them since developed under a different staff it borrowed from/copies gameplay from SF1. Honestly outside of better/smoother controls and more interesting characters and visuals, and the ability to dizzy your opponent, Street Fighter 2 hardly innovates at all from SF1.
5. On the topic of Time Killers. Time Killers in no way borrows from Street Fighter 2 in character design, control scheme, plot, visuals, nor audio. Time Killers presented a very mature/brutal fighting theme involving dismemberment. For its credit, the game did not copy off of Mortal Kombat neither. Time Killers was developed and released around the same time as MK. Time Killers control scheme involves the direct use of the left and right limbs and head. Pressing both arm or leg buttons results in added attacks that use both limbs.
Also worth noting. Visually, on a technical level, and though many wont agree due to personal preference of Japanese versus American style artwork, Time Killers also visually surpasses most games released during its time period due to its 32-bit visuals (Large characters, vivid higher resolution graphics). The hardware also used an advanced sound chip by Ensoniq, who made the Ensoniq Soundscape audio card. Spec wise CPS-1 couldn't not keep up with Strata's hardware. This same hardware powered Blood Storm and Street Fighter :The movie (the arcade ver., not the shit home version)
6. If Samurai Showdown borrows from anything besides Street Fighter 1, it would be Time Killers and also Blandia (the sequel to Gladiator from 1986).
