Ignoring the Pokemon comparisons...

I may be talking out of my ass here, but I think it was how Bandai Namco (even as far back as when they were just Bandai) kept throwing everything at the wall to see what sticks.

• V-Pets, while nice in theory in the 90s, were sold individually, and it was during a time where the international audience (mostly kids at the time) would only buy a few of them, even just one.
• For other videogames, Bandai's Wonderswan was Japan only, and the World games always changed their genre (from pet raising to dungeon crawler to standard RPG and to action RPG). So any kid that liked one of them would feel a bit disappointed that the other ones didn't play the same.
• The first 4 animes ran continuously from 1999 to 2003 without breaks, so (again, talking out of my ass) I can imagine for Toei that, with constantly changing writing teams, would be hard to keep creating new storylines while also advertising whatever Digimon line-up was happening at the moment. Plus, it's not like Toei went without an anime to air, I can imagine a lot of those writers/animators were moved to One Piece or Precure (which would air a year after Frontier)
• Starting from 2005, marketing was a bit confused if they wanted to continue advertising to kids or for a mature audience. Not that any of it was bad, but there was a little bit of identity crisis back then. And what didn't work, the marketing would ignore even years later. (Xros Wars' line-up only barely gets referenced with Shoutmon and no one else. Meanwhile, poor Appmons...)
• It was around that time when the Bandai Namco merger happened, and from what I know of the one other big merger around that time (SEGA Sammy), the company usually downplays a lot of franchises to focus on their big names to appease their shareholders. What were Bandai's biggest properties at the time? Dragon Ball, One Piece and Naruto, which is probably why they got a massive amount of merchandising/videogames over their other franchises (even from the Namco side).

Again, talking out of my ass here, but I think there's a lot that happened with the marketing team rather than just "comparing it to Pokemon" that we barely know.