Similarities between Kanto and Unova

[Joshawott]

The existence of a Fire/Lighting/Ice Trio, I guess, could also be a similarity.

Not to mention a flying-type legendary trio (Tornadus/Thundurus/Landorus), and a legendary Pokémon that was modified by science (Mewtwo in Kanto, Genesect in BW) - extending into other media, Mewtwo was modified by Team Rocket, whereas Genesect was modified by Team Plasma; the villanious teams of their respective regions.

Then, the following:

Timburr line - Machop line
Roggenrola line - Geodude line
Throh & Sawk - Hitmonlee and Hitmonchan
Munna line - Drowsee Line
Woobat line - Zubat line
Drilbur line - Sandshrew line
Audino - Chansey
Tympole line - Poliwag line
Trubbish line - Grimer line
Frillish line - Tentacool line
Klink line - Magnemite line
Bouffalant - Tauros
(Excluded things like Pidove line and Patrat line, as every region has some of those...)

Although each odd-numbered generation has added two fossil Pokémon, Tirtouga's line shares its types with both the Omanyte and Kabuto lines of Kanto.

Kanto and Unova are also the only regions to feature badge-check gates before Victory Road.

Also, what's interesting to note, is that Blaine (Kanto's 7th Gym Leader) was inspired to train Fire-type Pokémon after getting lost in a freezing mountain range. Brycen (Unova's 7th Gym Leader) trains Ice-types, and his gym is located inside a mountain.

Both regions have a Fighting and Ghost member of the Elite 4, while the initial champion is your main rival.