Well, without knowing what shortcomings it might have, I'd start with tires. The factory never knows where you'll be riding, so they may spec some sweet tires for hardpack, but you ride in loose sand, gravel, or exceptionally rocky terrain.
Seat, bars, grips, and pedals are other items frequently swapped out. Depends on what works and what doesn't.
Depends on what you want to accomplish. IMO, the best area to upgrade
most entry to mid level mtn bikes is wheels. Most manufacturers tend to spec heavy machine built wheels to keep cost down. If you want to make your bike lighter and faster, reducing rotating weight is the first place to look. Of course, wheels will also probably be the most expensive upgrade. A nice set of hand built wheels can cost as much, or more than you paid for your complete bike.
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