For a brand new bike, the only things I would ever consider "upgrading" would be from the following list.
1) Saddle
2) bar ends/grips
3) Pedals
Anything else that I would be concerned with upgrading right away would keep me from buying the bike in the first place since it isn't cost effective.
Edit: I would consider brake pads and other consumables for changes too.
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Slow Ride Cyclists of NEPA
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