This may be perceived as a non-objective review but nevertheless, I would like to share my opinion on why I will always choose Water-Based Acrylic Pen over an Oil-Based sharpie any time of the day despite its flaws.
Proponents of the Sharpie argue that the oil-based ink soaks into the absorbent midsole resulting in a permanent whitening of the sole. It will also have no cracking issues, which is commonly found in Water-Based Acrylic pens.
However, a fatal flaw of the Sharpie is that it leaves a very noticeable glossy finish on the midsole which makes it looks fake, which is what you want to avoid in the first place. We did not spend hundreds of dollars on precious pair of sneakers, only to scrimp a few dollars on a sharpie pen and permanently make it look fake. Don't believe me? Look at the picture below. I used a sharpie pen and now my Air Max midsole has a gloss finish. If I used this on an Ultra Boost, I would have probably thrown them out by now.
When you compare it to the area which I applied a Water-Based Acrylic Pen, you can see a very noticeable difference. The Water-Based Acrylic Pen blends perfectly with the original midsole as it leaves a matte finish instead of a gloss finish. Especially on BOOST midsole, which has an original matte finish, you would not want a glossy finish on them.
If you use a high quality Water-Based Acrylic Pen, the paint is highly flexible which means that it does not crack easily and can easily last you a few months before you see any noticeable cracking on the midsole. When that happens, you can easily touch it up with a few strokes of the pen.