I wonder how the idea of Catherine having a steady relationship with a new character came to be. NecoJi would have been created after the military premise was discarded so it's unlikely that Catherine being in a relationship was originally planned.
Catherine doesn't play the role of the love interest, as Blinx is smitten with Princess Lena. Her role is strictly limited to the cute shopkeeper in BLiNX 1. Really there's not much point to her having a relationship at all when the games already had Blinx/Lena and Benito/Mina.
1) My guess is that Artoon needed an excuse for Catherine to make a cutscene appearance in BLiNX 2 (as she no longer had her role as a military nurse) so they had NecoJi propose to her.
2) Alternatively, someone at Artoon spontaneously thought that it would be cute if Catherine got into a long-term romantic relationship with someone. It's possible that NecoJi's personality was influenced by this. I'm probably just overthinking, but I think it adds to how cute and wholesome NecoJi and Catherine are as a couple in my eyes.