No, neither the rarity of certain Pokemon nor the way they are presented in the Pokedex needs to change.
While the Internet and SPP obviates this as you mentioned, for those skeptics and the uninitiated, I would still like the game to provide you all the clues as to these Pokemon's whereabouts. The vessel I feel would be most appropriate for the relaying of this information would be the NPCs in the game, those just standing about on routes and asking for a challenge or none at all.
I'm sure that many of you skip over most of these people since you feel they aren't important, and I'm willing to bet that most others do - though not I - however, this plan will put them to good use. Instead of all of them dragging on about how they haven't found some ancient ruins that probably don't exist in ten, twenty, thirty, or even fourty years, the overwhelming majority will employ that tactic of tedium. Yet, a few anointed individuals will give you some useful advice. For instance:
"Have you ever heard of that Pokemon PERAP? They say it's impossible to find in the wild, but I swear they're lying! I found one right at the top of Mount Cobalt. Take a look-see, I'm sure you'll find one yourself! Bring it back to me so my suspicions can be confirmed."
This would get you a Nugget or something, but that's not important: what's important is that the game is providing you with some of the help you need. Of course, it wouldn't do this for every Pokemon, at least not that directly: it might say that some dragons lurk deep in that cavern, but not make any reference to a particular species. Hints like this will drive you to think about the game much more than your Pokedex; be happy and fire your neurons.
