I feel like a lot of you that have this image of the Adept don't play Shadowrun. Shadowrun Adepts are THE badass unarmed warriors that have channeled their magic power internally to gain martial ability.
Tossing tool proficiency away entirely. Maybe doing a background system, in the style of 13th age, if you absolutely need something to stand in for it, but think all tool uses should be folded into existing skills. You might need to add 2 or 3 new skills to cover it, but I can't think of a good...
Two things that I personally love are the stacking/subtracting boon and bane mechanics from Shadow of the Demon Lord and a method to expend your advantage for an effect.
So, huge issue with advantage/disadvantage for me is the binary nature of it. Oh, your elf fighter has been blinded...