So like, in my opinion, it depends on what we mean by skill. If we’re talking solely martial arts, or including Ki.
If it’s solely martial arts, they’re about even? You have to remember that GTku is also Toeiku, which means a lot of his skill feats aren’t from GT. (And not many exist in GT, to be honest.)
So, for example, GTku is at a level of skill that he can face 4 people just as strong and fast as himself (if not superior in stats) with superior martial arts knowledge to himself off raw skill alone (Goku V Perfected Multiform Cell), has directly went up against an individual who collects the entire memory of everyone he’s ever possessed (including their combat knowledge) and held up against him, albeit temporarily as his stamina made him unable to keep up in stats and caused his form to run out, (SSJ3 Goku V Baby Vegeta), can fight heroes who’ve been training for thousands of years (Afterlife Tournament), etc. GTku is also able to predict teleports and fight with that knowledge, which while not the same, (and SLOWER), is similar to predicting Hit’s Time Skip.
If we’re talking explicitly Hax involved martial arts skill, like Ki, prrrrobably Super Goku. GTku isn’t a slouch—He has the precise Ki Control to utilize Super Saiyan and Kaioken at once, can automatically counter techniques just by adapting his Ki to what he’s fighting against, (none of Omega Shenron’s hax abilities in his combo did damage because SSJ4 Goku adapted to all of them previously), and I think the best skill feat GTku has is adapting to and resisting absorption by simply hearing of Cell being able to absorb people. “Hearing” being his own mental awareness while sleeping and being told Cell could. That, plus the inherent regulation of Ki with his tail that amplifies precision and reduces drain makes me believe GTku is the more precise between the two of them, and could probably do more if given the same tools Super Goku did.
However, that in itself doesn’t stack up to the skill of Super Goku, who figured out how to calculate the exact force and angle to nullify universe destroying attacks in 3 tries, mastered a martial art that has multi-million to billion year old gods stumped, can use his Ki in more creative ways (God Bind, Hakai, Destructioning Objects), etc.
However, in trade I think GTku is just a lot smarter than Super Goku. At least in terms of long form strategy. Him, Trunks, and Pan on two occasions were able to plan and create an opening to confront Baby (Planet Pital and Planet M2), by staging specific events in their own favor to get him to reveal himself. Then against Naturon Shenron, he played to the Shadow Dragon’s ego to save Pan from his absorption, and against Omega Shenron he was able to plan with Nuova Shenron to achieve a game winning guaranteed kill. It only failed because Omega revealed he had the power to possess other Shadow Dragons.
So in pure hands, even-ish? Skill as in Precision with Ki? GTku. Skill as in Hax with Ki? Superku. Actual Strategic Intelligence? GTku.
That’s just my opinion though.