TL;DR: Yes, you could argue that gen II is superior.
I suspect you could argue that any generation was the best generation. After all, "best" is very subjective, and there isn't really an objective way to say that "change X" is clearly better/more significant than "change Y." Disclaimer, gen II is my personal favorite, and I'm sure that nostalgia colors my perception of it. But can those who love gen III, or any other gen that they grew attached to during their childhood, genuinely say that their own memories have no bearing on their opinions?
That being said, here are some things that made gen II really stand out for me:
1. Two regions. Yes, I know a lot of people argue that Kanto was a watered-down, glorified gym rush, and certainly, I would have preferred a better-developed Kanto, but I remember my excitement upon vanquishing the Elite Four and Champion and discovering that eight new badges awaited me. I didn't find the leveling scheme in Johto that problematic (though perhaps that relates to my being young and relatively inexperienced), and I loved the region and the story. Johto offered a great deal of geographic diversity, from oceans to mountains, small towns to large cities, while Kanto offered the familiarity of RBY with some new touches.
2. In many ways, GSC were sequels to R/B. The continuity between the games' storylines was something not seen again until gen V, and as a player who put countless hours into Red before picking up Gold, that was something I greatly appreciated. The physical connectivity between Johto and Kanto helped with this, as did the Team Rocket plotline and the references to what had changed in the past three years. The final battle with Red was a great touch, too.
3. Backwards compatibility (sort of). Unlike later games, where you could only transfer forward from one generation to the next, the Time Capsule in GSC allowed you to trade both ways, assuming certain conditions were met (e.g., no new moves or Pokemon). This was a feature I took advantage of to complete my Pokedex in Gold, and then to complete my Pokedex in Red after Gold died and I was stuck with just Red (from which I had traded a lot of Pokemon to Gold before Gold died), a Silver with very little money or Pokemon of value, and an incomplete Yellow that I didn't want to rush through. (Eevee breeding, anyone?) This was also great for my last-ditch effort to make teams to beat Stadium as quickly as possible (elemental punches from Goldenrod Dept Store = quick and cheap way to diversify a moveset). Overall, I was much more reluctant to transfer Pokemon in later games, because such a move was so permanent. But at the time of GSC, all of the main Pokemon games could trade with each other (unlike after the gen III reset), which was great.
4. New mechanics. Every generation has new mechanics, and we could argue all day about which ones matter the most. But I would argue that breeding, and the introduction of elements like genders and egg moves, made one of the most significant changes to Pokemon. Making a competitive team no longer necessarily required playing through a game over and over again to get the requisite TMs, and there was now some control over stat inheritance. Certainly, breeding has become much easier and much more fleshed out over the years (I can now breed 5 IV Pokemon with egg moves and appropriate natures in very little time), but gen II started us down this road. Without breeding, competitive Pokemon as we know it today would have been very different. As for other mechanics, I personally loved the day/night cycle (even if it did drain my internal batteries far too quickly), and I have many fond (/tired) memories of waking up early to try to catch some morning-specific Pokemon. Stat changes, like splitting Special into SpA and SpD, certainly changed the game significantly as well, as did the introduction of new types. Although other generations have brought changes that have significantly altered the metagame (e.g., abilities or physical/special split), these ones certainly had an impact.
I'm sure that there are plenty of other elements that make gen II stand out, but unlike many years ago when I unwrapped Gold at a birthday party and began my journey into Johto with Totodile, I don't have the luxury of spending hours pondering them. The real world beckons. But the short answer is that yes, an argument can certainly be made for the superiority of gen II. That doesn't mean that gen II needs to be everyone's favorite generation, but the Pokemon world would have evolved differently without it.
I believe this post pretty much sums up what I would've said. The second generation I felt put more towards developing the franchise as a whole than most of the other games in the series, which is perhaps why I felt horribly underwhelmed with Ruby and Sapphire.
In addition to breeding, Pokemon Gold and Silver introduced several new mechanics that more or less have stayed relatively the same for over a decade.
1. Such as the 'Special' split between Special Attack and Special Defense, which granted an entire new depth into the game itself, giving us more numbers to play with and to compete against.
2. The ability to fight trainers multiple times through the PokeGear, so you weren't restricted to just wild Pokemon and the Elite Four.
3. The days of the week and the Night and Day cycles, which changed which Pokemon you could battle, and which trainers you could battle.
4. Contests and events were first introduced in Gold and Silver; the Bug Catching contest for example.
5. Items can now be held by Pokemon. This created worlds of new strategies that could make or break your victories.
6. Berries (Yes, berries although you couldn't grow them).
7. Shiny Pokemon, and without them I'm certain several of us on the boards here wouldn't collect nearly as much as we do.
8. Different ways to encounter Pokemon besides surfing, fishing, and walking.
9. The idea of backwards compatibility, and without it we might not be able to carry our precious Zubats and Ratattas with us every time they come out with a new game.
10. Mystery Gift and Pokemon Events, which we all use liberally to this day. We see several events around the world and Silver and Gold started this trend.
11. Gold and Silver were even capable with communicating with sources other than another gameboy with something akin to the PokeWalker (it starred Pickachu, like a tamigachi or something).
12. Customization first showed up in these games as well. The Bank of Mom would use money you saved to purchase cool items for your room like PokeDolls, furniture, and would even purchase other items for you. It's a feature that I always miss because it gives us some incentive to actually travel back and visit dear old Mom.
13. The Post-Game. Pokemon red, Blue, and Yellow had very little to the post-game other than to capture Mew-Two, it was much improved and I feel like this improvement translated well to the other games in the series.
14. Specialty Pokeballs were first introduced here as well, giving other, better ways to capture needed Pokemon at night, lower levels than you, during fishing, opposite gender Pokemon and other factors, such as raising kindness, that were so good that Ruby and Sapphire took them with their own purposes.
15. For better or worse, roaming Pokemon.
16. Baby Pokemon and 'senior' Pokemon. I feel that even though it makes sense, without Gold and Silver introducing Baby Pokemon and Pokemon with the ability to evolve further (Crobat, Chansey, Slowking, Steelix)
17. Evolutionary lines that diverge from one or two paths were introduced (for example Polytoed and Slowking)
18. Pokemon that evolved by Holding certain items when traded.
19. Pokemon that evolved through Happiness or at certain times during the day.
20. Two more types, Steel and Dark, which worked so well that they weren't joined by the fairy type until
15 years later.
??. and Shuckle. . . not much else to say there.
And several other features I'm sure I've forgotten over the years, but out of all the games I feel that Gold and Silver did the most work in terms of pushing the envelope and shaping the games as a whole. It gets my vote as the best simply because of all the work it did to broaden the scope with which we can view our Pokemon.