Back in the days of Generation 4, you needed to import Pokemon from Generation 3 in order to complete the National Pokedex. The Generation 5 titles seemed to reduce a lot of this, so is importing anything from the Generation 3 games even needed to complete the Pokedex in Generation 6?
Looking at http://www.serebii.net/xy/unobtainable.shtml, there are 27 Pokemon from Generation 3 that are listed as "Unobtainable" in X and Y. However, you can obtain a number of these through previous games.
If you own HG/SS, you can use the Pokewalker and the "Hoenn Starter" gift to get a majority of those 27 missing pokemon. You can catch Latias, Latios, Groudon, Kyogre, and Rayquaza in HG&SS as well, which takes care of a good chunk of the legendaries required to complete the National Dex.
The unobtainable list for HG/SS (http://www.serebii.net/heartgoldsoulsilver/unobtainable.shtml) lists only Regirock, Regice, Registeel, Jirachi and Deoxys as unobtainable, which means you can obtain 22 of the missing pokemon just from this game alone.
Using Black 2 and White 2, you could then catch Regirock, Registeel, and Regice, leaving Jirachi and Deoxys as the only two unobtainables.
This is where it gets tricky. If you participated in any of the events where Deoxys or Jirachi were handed out, then you would be able to bring the final two in from one of those games. However, if you missed out, you're going to have to wait until the next event where they hand out those pokemon. The only reason you would have to import them from Gen 3 would be if you had one of them on RSE (Like a Jirachi from the Pokemon Colosseum bonus disk). Otherwise, you could just wait for the next event, or get them from a previous event.
Hopefully, this will help you out in completing the National Pokedex. Good luck!
Short of events, the only Pokemon you need a Generation 3 game to get in Generation 6 is Jirachi. It was distributed in events in subsequent generations, but an add on for Pokemon Colosseum makes it possible to obtain Jirachi through normal gameplay if you interface a copy of Ruby and Sapphire to said add on.
The only other Pokemon from Generation 3 that is otherwise unobtainable is Deoxys, however that was never distributed outside of events so it is impossible to obtain it through normal gameplay in Generation 3 or any subsequent generation.