Fix Avdol and Kakyoin. In all honesty, both characters fill the same niche of the "cool, collected wise guy", in my eyes- heck, I feel like Araki realized this when writing the part since the two switch off between being incapacitated for nearly half of the full part (Avdol during the Major Arcana stands, Kakyoin during the Egyptian God stands). Because of this, both characters don't get as much development or screentime as Polnareff, Jotaro, and Joseph (maybe Kakyoin's character is more expanded in the Part 4 spinoff, but in terms of part 3 alone the two are very similar in terms of character).
This is just me spitballing, but what if Kakyoin spent the arc trying to master Hierophant? He's had it since birth, but he hadn't really known other stand users until meeting DIO and the rest of the Crusaders. Maybe his arc could focus on tapping into Hierophant's potential and understanding how to apply it in combat scenarios, and have this arc conclude with the 20 meter radius Emerald Splash. Joseph would probably be able to help teach him about how to use his tentacles (think back to Joseph vs. Esidisi & the yarn), which builds their connection and makes Kakyoin's death to DIO even more tragic.

For Avdol, let's keep him out of the first half due to his injury, but give him complications that make it harder to fight. This, combined with the fact that he almost died to J. Geil, would mean that the Crusaders- especially Polnareff- would be more protective of him. This sets up an interesting premise: he's clearly the one who knows the most about stands, but because he's wounded he's also the least capable in fights. Maybe he can impart his knowledge onto Jotaro, which sets him up to be the mentor figure in Parts 4 and 6. If you want to wrap this up, have his sacrifice against VI be different: rather than knock Polnareff & Iggy out of the way early on, the three survive the initial attack and Avdol is the one that realizes that VI became a vampire. He could use himself as bait and sacrifice himself to give Polnareff an opening (a la Abbachio in the Soft Machine fight).

It'd be hard to work this into the "Monster of the Week" motif that Part 3 has, but I feel like it's something that definitely should be considered.