When choosing an engine there should be one additional 'factory' option. This engine has the lowest specs at the beginning but should be the only engine you can develop. For customer engines your upgrades should be dependent on the supplier team. You should however be able to develop fuel related upgrades as you can have a different fuel supplier.
Engine upgrades shouldn't be immediate, they will only work when you swap out an old engine part for a newer spec part.
As a new team you might also opt to 'buy' a chassis instead of manufacturing it yourself, like Haas with Dallara. Also perhaps renting facilities like the wind tunnel to cut costs.
You should be able to hire a chief designer, which will have effect on upgrades too (higher rake, drag focussed, aero focussed, etc.) As design philosophy is quite important in F1.
Being able to choose from multiple nose designs, each with different perks (and looks).
Test/Sim drivers, which you can allocate free practice time (I always skip one training).
Partnerships with F2 teams so you can have a test driver develop himself there, and during FP in your team, this will however cost you some money.
During free practice you get these additional sensors, or flow viz on the car to give it more of a real free practice feel. Depending on your facilities these can also look different or more complicated.
A bigger driver roster which also has some ex-drivers that are not officially retired or currently in a different series (hulk, vettel (?), Wehrlein, etc)
Being able to change the focus of development on the current or next years car
Kimi Raikonen having issues with the drink.
