I can't say I can fully relate to how you feel, but I understand completely.
There was a thread on here from someone who had Risa Kamizaki from Amagami as their waifu. I know the series pretty well, so I knew about her myself. She had three appearances in two seasons in the anime, and in two of these appearances she wasn't even central to the plot.
For me it was a bit of a reality check. I felt really bad for wishing that mai waifu had more than just cameo appearances in the first nine episodes in her series, or had more fan art, and felt relatively fortunate.
All I can say is to not be deterred by the lack of canon for your waifu. The ability to form it yourself has its upsides.
>I can see why someone would consider it to be shallow since one can basically take a character such as this and mold it into their ideal partner.
There are plenty of people out there who have Hatsune Miku, and the other vocaloid characters as a waifu/husbando, and none of them have a set personality. I don't find it a bad thing, personally.