My main issue is that one medium is trying to work with another, when they're really meant to be separate (3D and 2D in this case). It's like adding a tomato to a fruit salad - yes, they're both artistic mediums, they can be used together in some rare cases where innovation takes the lead, but for the most part, you wouldn't try and mix the two unless you were going for weird results.
Using 2D in 3D environments can work... sometimes. It depends how well they work together in terms of style. An example of 2D assets that work well in 3D environments? Look no further than the Gorillaz. But the way the art is presented gives it the same dull, dark look as their environments, meaning that the two mediums work together rather than against each other.
That's not to say there aren't places where it doesn't look awkward, but you have to find that middle ground.
When you do a 3D comic, you're inserting 3D models into a restricted 2D environment, including the 2D panels, the 2D (and often intrusive when places over speech bubbles) speech bubbles, and 2D rendering (including lighting, shaders, etc. that are often done in 3D renderings and are behind the scenes). Mix in the fact that 3D doesn't leave much to the imagination and 2D is more about suggesting form, and the hundreds of uses of stock models and amateur modelers who've probably only ever used MikuMiku Dance, and you've got yourself a recipe for a horrible 3D comic experience.
So how can you make a good 3D comic?
First off, find that happy medium. Maybe instead of just plopping 3D assets into a 2D world and arranging them to your liking, find a way for them to mesh into the actual environment. Use your brush tools to paint over them, don't let them just sit on top of the panels.
Here's a classic and good example of how 3D assets can be used to create a beautiful scene in a painted 2D comic:
Notice how the 3D objects don't just "sit" in the scene. They've been blurred, painted over, manipulated in a fashion where they still retain their 3D integrity, but don't compromise the composition as a whole.
What also goes into making a good 3D comic? Accepting the fact that it's a comic - you will have to draw. Even 3D animators are taught how to animate in 2D first before they move onto 3D - if it's an artistic medium that is performed on a canvas and represents an illustration, you will have to draw. If you don't know how to draw, then you have to accept this as well - but don't use it as an excuse to deliver work that's less than what you would strive for. Rather, use it as an opportunity to learn - even 3D modelers have to learn how to draw to some extent (it's like expecting going into the film industry as a boom mic operator but not knowing how to use a video camera - you're still going to have to learn things pertaining to the industry as a whole even if it's not your main job.)
Take the time to make it look good. Use that extra hour to clean up areas where the 3D assets clip, to paint over the skin tones and make them more realistic, to make that character fit into their environment (rather than getting thrown into it). The general consensus by most is that because you can make 3D models once and be done with it from that point on, they're easier and "more convenient" to make than 2D comics. While this is true to some small degree (yes, once you've made a 3D model, you won't have to remake it for a long while, unless you lose the model or have to redo it or add something onto it), it still requires your full effort. Don't half-ass it just because everyone else is.
Finally, know that the path you've chosen by meshing 3D and 2D is not an easy one. You're trying to adapt one medium for another. This can bring its hindrances, but it can be innovative and unique at its best. You're going to have to end up putting in effort to begin with, so you may as well make it your best.
