You should avoid adding most upgrades to your helicopter when learning to hover. The main reason for this is to avoid creating a "hangar queen".
A "hangar queen" is a fancy helicopter which has so many expensive upgrades that you are afraid to fly it (or try new things) because you may crash the heli and damage the upgrade parts. Therefore, it sits on a shelf looking pretty, and is rarely (if ever) flown. This sounds silly, but this is a very common beginner syndrome.
If you want to learn to hover well, it is best to create a "workhorse" heli which you are not afraid to crash. You should consider your R/C helicopter interest from a long-term perspective and understand that you will eventually own more than one helicopter, and that your first helicopter is mainly a tool for building basic hovering and forward flight skills. While you are building these skills, you will probably crash many times. Therefore you should create a first heli to which you are not financially (or emotionally) attached, and are not afraid to crash.
However, some upgrades are justifiable to beginners. Some of these upgrades are:
Some stock swashplates (such as the ECO 8) are easily damaged in a crash. Some metal swashplates are only 3 times the cost of a stock swashplate, and are much less likely to be damaged in a crash, so a metal swashplate is sometimes justifiable.
Tail servo mount
Tail servo mounts are usually better with heading hold gyros than the stock servo mount because it reduces the slop (and can eliminate tail wag) by minimizing the distance and slop to the tail pitch lever.
Carbon fiber pushrod for tail servo
These improve tail control and are easily damaged in a crash, but they cost only about $3 to replace, so are justifiable.
An autorotation gear is usually required when a brushless motor is used (except for some helis like the Corona). A brushless motor has a very strong braking force when the throttle is reduced, and the motor pinion will strip some teeth from the main gear unless the main gear has a one-way bearing installed.
A ball-in-swash modification converts a floating swashplate (found on some older helicopters) to a rigidly held swashplate. This improves cyclic control and makes learning hovering easier.