Honestly, I've been playing the series from the start and I feel the newest generation is the best yet, followed by Hoenn, Kanto, and Johto in dead last. I just can't think of any interesting pokemon from Johto, especially not the starters. Johto's starters were incredibly minimalist, having few details and changing very little as they evolved. Their heads seem to be the only part of their body to go through any major change. As if to add insult to injury the majority of them, starters included, had incredibly piss poor stats.
By the way, that vgcats comic strikes me as being a parody of people recalling the 'good old days' of pokemon, comparing people who think the first games were the best to a bunch of old men. Appropriate if you ask me. While the series hasn't deviated from the formula much (which is reason enough to question how any previous game could be better than the newer ones, since the newer ones still have the same features) its really come a long way. After beating the Elite Four in R/B/Y there was nothing to do except catching all the pokemon. G/S/C did little to change this too, choosing to drag the game out further instead of actually adding anything. It wasn't until R/S/E that they started adding in more mini-games and sidequests, and they expanded on this in D/P/Pt. The series has pretty much evolved into a sandbox rpg now, giving players a plethora of sidequests, mini-games, etc.
Playing pokemon just to get all the badges and beat the Elite Four is like playing GTA just to progress through its story mode, which is what some people seem to want given the way G/S/C's addition of Kanto is praised. It does seem quite likely that G/S/C will be getting a remake at this point, what with the poster for the next movie showcasing Johto's starters plus that 'notched ear Pichu', and I certainly hope they take the time to flesh the games out. Remodel the dungeons, LESS FETCH QUESTS, and either make going to Kanto worthwhile (maybe by, say, putting the Safari Zone back in) or remove it altogether. Also, the new pokemon need to be in it and available early. The only pokemon that were worth catching in G/S/C were the ones from the 1st generation...