There is also one more added benefit for having common ground and pull-up data lines (over having common VCC and pull-down):
Even if the original intention was to connect devices on the same PCB at span of few inches only, it was successful enought so now is not uncommon to have the lines long couple of feets and connecting "devices" which could be computers or something of equal complexity, with some devices having its own power sources (of different quality, say you connect something wall-plug powered with something battery powered). It is better, if connection works "at least good" even in not ideal and out-of-spec conditions.
And lot of such connected devices may be somehow connected also by other means, then only I2C communication. Usually when connecting devices together you connect it with
common ground - sometimes as part of other functions, sometimes just because it is mounted on metal case and the devices are ground-connected with the case too (or with common cooler or something like that) or there may be shielded cable with grounded shield inside - which also connects the grounds.
If you also directly connect power lines (VCC) of such devices, you will get problems when those lines would be on different voltage naturally (sure, it may say 5V here and there, but depending on the construction and part tolerancies of power sources it could be also 4.9V or 5.2V or even changing, if it is battery powered and sometimes running some motors, making the power drop and rise over time).
In such case there is effectively short circuit betwenn those power sources of part a Volt and depending on the sources (and resistance of the ways) there could flow relatively high currents resulting not only in energy waste and heat rising, but maybe even in damaging (or shortening life) of some of those sources. Which is not good.
Having common ground and pull-ups avoids such problems - ground is ground and pullup resistors allow for only really small cross current even if the VCC differs a lot over the devices.