It depends on what kit you're ordering, but there are quite a few threads already about various deletes and swaps for the wings and fuselage. Personally, here's what I swapped in both:
Wings
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Swap fuel caps with deluxe locking caps - Personal preference
Nothing really else, a few o-rings in various spots to ethanol-proof the fuel caps and drain valves. They can be found in another thread on VAF here.
Add JD Air's drain valve and vent fairings
Fuselage
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Delete Brake Master Cylinders - BRAKE MAST. CYL.LEFT-1 & BRAKE MAST. CYL.RGHT-1 - Replace with Grove master cylinders.
Delete Brake Master Reservoirs - BAG 670 - Replace with Grove master reservoir.
Add right-side ELT mounting bracket - ELT/PWR MOUNT 7/9-R
Delete fuel valve - BAG 487 - This is because I need to go with a duplex Andair valve for my fuel injection system.
Delete all fuel, brake, vent, etc lines - Go with flexible Teflon hoses from Tom & TS Flightlines, or Bonaco. Or at the very least, replace with stronger aluminum tubing.
AT0-032X1/4X19'
ATO-032X1/4X12'
PT-062X1/4X9'
AT0-035X3/8X12'
Delete VENT SV-5 vents from VENT SV-COMBO X2 - Replace with nicer ones, especially Stein's