CGI was not as limited as you think in 1999. Look up films from that year and you’ll see.
Interesting anecdote I heard: Shake was up for an Academy Award, but Apple pissed off the wrong customer when they discontinued the Windows version (which was used for The Matrix). I won't name the post house, but the owner reportedly sat on the academy's technical committee and tanked Shake's nomination as punishment. Kinda sucked for the team, who of course were blameless.