The place where they both began. Both work off simple concepts to reach their goals. Both work off their respective series' simplest designs and mechanics. Both focus more on the sense of basic, shonen adventure than their successors. Both introduce an aesthetic that is mirrored in later installments (Red's ballcap/ Tai's goggles).
Generation II/Adventure 02
The time at which each franchise took what worked before and expanded it massively (item holding, eggs, and new evos/prevos for Pokémon; Armor Evolutions and Jogress/DNA Evolutions for Digimon. Both use protagonists that resemble hipper, cooler versions of their predecessors (Ethan and Davis/Daisuke). Both are heavily reliant on the previous generation (Kanto being acessible, many old Pokémon being prominent; all previous protagonists appearing in Adventure 02. Both are still regarded by many as the apex of their respective series, although some believe it to be much weaker than other efforts.
A bit of a falling-off point for fans, as both entries almost completely discarded what had come before. Both introduced new -although slightly frivolous- mechanics (contests for Pokémon; the Card Slash technique for Digimon). Both tackle heavier themes (the first real appearance of Godlike Pokémon, as well as environmentalism; Tamers' plotline dealing more with death, tied to Evangelion-esque angstiness). I suppose you could also draw parallels between Ryo and Fr/Lg (both are callbacks to the original generations). By the way, I
think this is where each franchise peaked, but that really doesn't matter here.
This is pretty much where the similarities become scarce. Gen IV is regarded as somewhat weak by many fans, but it isn't reviled in the same way Frontier was. Although Bidoof
might constitute a decent argument against this.
Generation V/Data Squad/Savers
Both tried to take the series in new directions. Both are regarded as a step behind usual efforts by some fans, although, as with Frontier, Black and White aren't nearly
as hated as Data Squad/Savers.
It's really too bad there's nothing to compare Xros Wars to. Ah, well.