I would concur that a custom micro coil cotton rebuild of the Protank coils will yield significantly better results than stock, but you can get even further down the flavor spectrum by using other gear. I don't think there's a good way to completely eliminate the flavor muting you expeirence in Protank style coils, I think it has to do with the airflow and how it has to wick.
In my opinion and experience, the best yield of flavor comes from RDA's, or dripping atomizers. Although you can get very close, if not indistinguishable results from RBA's (e.g. Kayfun series), they tend to be a little more on the maintenance side than RDA's. Building coils for an RDA is super simple, far easier than any Protank or what have you....it's pretty much wrap and screw. I don't find dripping inconvenient at all, but it's not something I'd want to be doing at work or anything like that.
I personally use all of the above methods. I mostly use RDA's/RBA's at home and custom coils in my mini-pro's for on the go. This works well for me and has for quite awhile now, I don't see myself changing anytime soon. I am pretty satisfied with the Nautilus I got in, but I haven't decided whether I feel it's good enough to completely replace my existing investment into the mini-pro's.