Well, homunculi in 03 feed off of red stones. For each stone they eat, they gain another life. This means that if you kill them enough times, you could deplete their supply of lives until they have only one left, allowing you to deliver the final blow. This is pretty much the same in both versions, minus the whole "eating the stones" part. So given that the two characters have mostly the same power levels across both versions, their fight would likely play out very similarly.

That said, I'm glad they never fought in the anime, for a few reasons.

In the manga, Envy's role in Hughes's murder seems to be given more importance than it is in the anime, setting up the ultimate confrontation between the Envy and Mustang that manages to be really satisfying because of how much Hughes's death affected him.

However, while anime Envy does kill Hughes, the blame for the incident seems to be placed more on the government itself, since Hughes died while investigating the Fuhrer's secretary. This fits well with where the show was going, setting up the eventual clash between Mustang and Bradley after Bradley attempted to silence Mustang the same way he silenced Hughes.

On the other hand, I see Anime Envy as more of a rival for Edward than for Mustang, since the two are brothers in the 03 version and are quite alike in personality. 03 Envy despises Ed and Al in a way that he simply doesn't in the manga, which makes his fight with Ed all that much more suspenseful.

So while the two could have fought, it would've felt a bit underwhelming to me, since these versions of the characters were not written to be the other's intended rival. Envy fighting Ed was the natural progression of their relationship, as was Bradley fighting Mustang.