I managed to legit complete the Pokedex in Pearl but after that any attempt to complete it in following versions was like pissing against the wind.

But I guess Yoyo's right. We've fallen out of Nintendo's target audience but I disagree with you comparing the evolution of the Mario title to the evolution of the Pokemon title.

Mario game changes from then to now is better graphics, some mechanics and some additional enemies and items (there would be much more to it than this but those are the striking changes). This is the same as the remakes of Heartgold and Soulsilver.
If, however, Nintendo started spitting out new Super Mario Bros games that suddenly included all of Marios family and extended family and mafioso second cousins and stuff then I'd compare that to the new Pokemon games.
Maybe it's just because people don't feel comfortable with what they don't know. I used to play Minecraft but I stopped because of the sheer amount of new stuff they were piling into it and I just got overwhelmed. Could be that.