why is my home value less than my neighbors when I have more up grades?

Also, Zillow doesn't necessarily know about all of your upgrades and so they are not factored in.  Your granite countertops, skylights, professional landscaping and finished basement would be very attractive to potential buyers, but your neighbors' two-car garage (versus your one) and extra 200 square feet make Zillow's algorithms value their house more.

Those are obviously just hypothetical examples.  :-)

According to Zillow, I overpaid for my house by $44,000, even though there were other bidders who were $25,000 and more over me.  The sellers had an unusual attraction to their house and thought my family and me would be better "stewards" of it than the other buyers.  Then, within a few months, a relatively run-down home down the street that Zillow had priced higher than mine sold for less than mine.  It was because mine had curb appeal (and significant upgrades) and that one didn't, and Zillow doesn't take that into account.

Upgrades are not the only factor in a home's value. More important things like square footage, number of bedrooms and baths, garage/no garage...these can impact the value greatly. Also location - corner lot, cul-de-sac.