I indeed find the Contracts a cheap power up method, or at least Gon's, given how easy they seem to be to learn for those who know of them and provide an unfair advantage against opponents (at least until I see a villain actually using one). Kurapika's abilities were handled OK in the Yorknew Arc due to their limitations, even if he was virtually unbeatable against a Troupe member 1 on 1 without much training because of it, though his myriad of abilities in the current arc seems to have made him close to a Gary Stu.
Also with Nen, we aren't given an in-depth knowledge as to it's actual creation or origin beyond the opening of pores, such as the logic behind contracts even being a thing.
Because of that, I'd say Alchemy from FMA is a better power system due to being more balanced and has more pseudo-science behind it. Despite it's flaws though, Nen is still the runner up for best/most interesting power system in anime/manga.