I feel that people are less upset about the actual placement of the games on the timeline than the fact that the official timeline killed the timeline theories that used to dominate Zelda discussions on various forums.
Aside from that, the major complaint I have seen is people claiming the downfall timeline was a cop-out on Nintendo's part as most people assumed only the Child and Adult Timelines existed prior to the release of the Hyrule Historia.
Exactly. The Official Zelda Timeline killed off timeline theories. Prior to it, a big draw to Zelda theorizing was making timeline theories. With an official timeline established, that type of theorizing became pointless (except for headcanon theorists). I remember people saying that Zelda theorizing died. For awhile it did lose popularity, atleast on this Forum it did for awhile.
However, sometimes I think what really happened was having an official timeline to agree on leveled the playing feild, and weeded out the decent theorists from the ones who really had no idea what they were talking about. There is no longer any hiding behind having a different version of the timeline. Ultimately what most theories came down to back then was a debate on each person's timeline theory, and I always felt it majorly took away from the main topic that was supposed to be discussed. Plus, having a different timeline theory could be flexible, so theorists used to be able to stretch certain theories by working their timeline theory to fit them. Now there is a solid framework to refer to, so one really must know what they are talking about to be a Zelda theorist. And to an extent, a decent theorist can be more spot on with theories, if they know what they are doing.