While 2D is certainly "based" on 3D, there is a fundamental difference that solidifies my preference deeply. Sorry if this is not directly related but I think it's worth saying.
2D love is very predictable. Some may find it a drawback, but I find it the opposite. The great thing about having a waifu is that, while you may have to find answers about the character you love yourself, there are pretty much only two options for your waifu's development, and both are fairly predictable. One is that she will never change from the perception that you fell in love with, and the other is that she will change with you. In either case, she is likely to stay close to your ideal - unless YOU change drastically in ways that you don't expect, which brings me to my point.
3D change in unpredictable ways. I mean sure there are going to be things that are "predictable" because humans are that way, but at the end of the day, you are not the 3D that you are dating, nor can you look into their head and understand their inner mechanisms. People can respond to the same situation in many different ways, and grow similarly. Sure, while there are patterns that you can observe and guess how a person will grow based on their past, they are ultimately in control of their future and how they grow as a person.
To be blunt, waifu are fictional, or at the very least you have found her through a work of fiction. Once her story is ended, you have two options: continue her story for her, or admire her story over and over again. Either way, you are the one in control of her growth, and there's a sense of stability in that that you won't get with a 3D relationship (unless said relationship is extremely unhealthy).
Of course there are other perks, like 2D looking much better than 3D, and having many traits that I admire, but the main draw for me is the predictability.