What kind of design freedom can you permit yourself in academic writing?
I read papers, I don't hang them on my wall. That is the main objective, and your design should subdue to it. I enjoy a well crafted book, but I get extremely annoyed when some unnecessary decoration gets in the way of usage.

In your case, the font of the titles requires a mental effort from my part to read them, which I find unacceptable, and thus, annoying. When reading a paper, I usually skim through the sections to get a broad picture of it; with Pacifico, I need to waste neurons in deciphering it while constructing my mental idea. I also find that the numbers in the text stand out a lot, probably more than they should, as they are not information I would like to get while skimming.

On the other hand, I have encountered a few unique and very nicely crafted documents, and those made a more long lasting impression. If not for anything else, I remember the general image of the article. 

Bottomline is, if your design is good, it will be welcomed; but if it has flaws, some picky people like me* may get displeased and cause a worse first impression. A standard template is a safer option; but more difficult to stand out.



*To give you an idea of how much, I find several citation styles to be rather annoying because they are clearly inferior to others. For example, anything without DOI in the modern times.