What are the things that you will usually replace in a ARF kit ?

For me, I would strengthen the joints of Epoxy and CA. Note: CA are expensive and probably factory will try to skimp on that.
I would also replaces the Clevises and pushrods (if they are bent).
Replace the fuel tank with Du-Bro. Check for air leak.
Seal any exposed balsa with clear covering.
Make the planes lighter and drilling holes through low-stress frames.
Sometimes, replace the motor mount with Dave Brown mounts and even re-construct the firewall if necessary.

Some ARF's just come with better quality hardware then others. I just go through the kit and see what looks usable and what needs to be replaced. Normally always like to replace the fuel tank even though the supplied one might work. I guess it's more a habit. I like to use carbon fiber as pushrods on my planes. Hinges are tossed out also most of the times. Of course you must look for weak spots and then fix or re-glue. I also replace the engine mounts on some of them. If the wheels are to heavy they are exchanged too.
That's about it.

Modern ARFs are getting much better then earlier ones. some of the new ARFs need no parts replacement.

Generally you will want to improve fuelproofing at the firewall. One quick sprayed coat of whatever it is that they apply just isn't adequate. Paint it with 2 hour epoxy and you KNOW its fuelproof.

I've got one example of a plane that needs no replacemts, unless you are sticking on an oversize engine. The Great Planes Fokker Dr1. Even the fuelproofing on this one needed no help. (very rare... I didn't paint the firewall with epoxy on this one.) My plane is mow over 1 1/2 years old, has had over 10 gallons through the .91 4-stroke I put on (oversize engine...) and it has put up with an amazing amount of abuse. Yes... when I landed on the wingtips I had to do major repairs... but thats kind of expected.

L8r... going triplane flying.

******

I might add... For a Lanier Comet or Slow Comet... you start by replacing the wings... then you replace the fuselage.... (its ALL junk)

I have to agree that things are getting much better. Case and point - I am about finished with the U-Can Do by G.P. The first thing I noticed was how well packaged this model was in the box. G.P. did an outstanding job. Ply braces on the sides and ends with foam attached to the ends so as to not damage the wing tips. I had never seen this with any ARF before. The covering was perfect and very neat. The engine mounting holes were pre-drilled with the blind nuts inserted and glued. The pre-drilled holes actually lined up with the aluminum engine mount I purchased for the O.S. 91 four stroke. Shocked and lucky things aligned. The directions have been simplified into pages rather than a book. Good for someone more experienced, but maybe not good for someone with little to no experience. Fuel proofing was already done to the firewall too.

I always reinforce joints, wing hold down and engine mounts. I just fibergalssed the wing in the middle on both sides to add strength. When I took the covering off I noticed a cracked piece of balsa in a bad spot. Hm........ glad this was caught early.

See pictures below of the fiberglass added on the bottom side before covering with the belly pan and then the topside, done the same way and then covered. The LG does seem a bit flimsy with only two screws holding it in place. From what I have seen as to how this airplane flies and lands, this most likely won't be an issue, but I would have liked the L.G. to be more secured. The horizontal stab has two socket head machine screws that go into blind nuts in the fuse. Nice added touch, but I still used epoxy just to be sure. Also added a Hayes 13 oz tank and exchanged the foam wheels for 3" H-9 Rubber Pro Lites. Replaced the 256 rods with 440's and used Sullivan solder clevises and Dubro threaded clevises on the adjustment side of the rods.