Despite the fact that I’ve been riding for about 15 years now, I still tend to buy bikes that many on this forum would call “entry level”. A decent entry level bike from a bike shop will be equip with components that will generally work fine if you are using the bike for it’s intended purpose (don’t take a Hardrock to the top of the local sky resort). There will inevitably be some weak points and/or things you don’t like about the bike. This has pretty much already been said, but as you ride and discover the weaknesses either by braking parts or noticing poor areas of performance, replace what is necessary. I don’t think you can make a definitive list of parts to upgrade because different bikes come with different parts, and different riding styles require performance from difference components. I replaced the rear derailleur on my bike, but I wouldn’t suggest everyone replace his or her derailleur. My OE derailleur smacked against my chain stay all the time and took too long to shift. Your bike might have come with a derailleur that was a better match to the bike and to your riding style and if you were to run out at upgrade it, you might be wasting your money.
I suppose most everyone needs a bottle cage, and if chipped paint on the chain stay will break your heart, you’ll need a protector.
