It's difficult to say which Toad is THE Toad. There may not actually be THE Toad. Red-Spot, Blue Vest (RSBV) Toads that appear in limited quantities only show up in the spin-off games for the most part. That Toad in particular may not be the same Toad every time. However, we must note that Toadette is probably the only Toadette since she is of limited quantity in every game she appears in.
In main series games, the RSBV Toads are generic allies with one running each Toad House, being Town NPCs, or being staff at Peach's castle. Meanwhile, a handful of Toads are indeed special in these games: Captain Toad & the Toad Brigade, Blue Toad, and Yellow Toad. Of all of these characters, Captain Toad is the most distinguished of all Toads even though he has not appeared in the spin-offs yet. He is now more special than ever because he has a playable role in 3D World and even a costume change. Originally sporting a red vest, his attire is now fully exploration based. This can only mean good news for him for the future.
Unfortunately, Captain's physical capabilities are lacking compared to Blue Toad and Yellow Toad, who have experience in tackling levels with the Mario Bros. Of these two, the Blue Toad has more experience and history, but this is only if we can assume that the Blue Toad in New Super Mario Bros. Wii/U is the same one as the one in 3D World. His design is generic, there are more than one Blue-Spot, Blue Vest Toads, and the only reasons that this Toad is blue in 3D world to begin with is to be a reference to Toad's SMB2 sprite and because it allows him to associate with a color other than Mario's trademark red.
So as you can see, it is very complicated to say that one Toad in particular is the main one. The RSBV Toad is most iconic, but is used as a meat shield for peach because that coloration is typically used for her castle staff. Captain Toad is a rising star, but is not as iconic as the generic Toad yet. 3D World's Blue Toad, if the same one that is playable in the NSMB series, is as capable of being a platforming hero as the Mario Bros. and Peach can. However, he is not as distinguished as Captain Toad, and I fear that Sakurai feels that because Toad plays so similarly to Mario and Luigi, that his inclusion would be redundant. But perhaps not. I think we have confidence issues if we think we can accurately predict Sakurai's final roster.