Imo upgrades having real utility makes or breaks this mechanic in most games. The upgrades need to be consistently useful to the player.
Other things to think about for base-upgrade mechanics:
Tiered upgrades - extend usefulness of existing upgrades, I hate when things get "left behind" or become obsolete if I spend any significant amount of time unlocking something.
Garden provides the ability to grow certain ingredients without venturing back into a "low level"/early area.
First tier only provides a few slots for ingredients, successive tiers provide more slots and more options for what to grow
Uniqueness
Base upgrades should be things that provide utility that is unobtainable anywhere else
Idle utility (think producing anything in Stardew)
Garden is a good example, grows while you're away and you don't have to worry about it. Or maybe you do have to worry about it until you get that {witchy version of a sprinkler} upgrade
Required upgrades for progressing through the story
Imo upgrades having real utility makes or breaks this mechanic in most games. The upgrades need to be consistently useful to the player. Other things to think about for base-upgrade mechanics: