There are several issues with the current implementation of the timer used in "Your Time"-based VGC timers. As a summary of how it should work:
Team Preview: 90 seconds. If time runs out, the game auto-selects the first four Pokemon by slots, or the first 4-n Pokemon if n Pokemon have already been selected.
Game timer: 45 second selection time, five minutes (300 seconds) of total selection time (Your Time) throughout the game. If time runs out at move selection, the Pokemon's first moveslot is chosen. In Doubles, if one Pokemon's move has already been selected and the time runs out before the other can be selected, the first selection counts, but the second unchosen selection defaults to the first moveslot as usual.
Current Issues:
The 90 second Team Preview timer is applied whenever the timer starts, rather than exclusively at Team Preview. This results in a user having 90 seconds of selection time if the timer was turned on at turn 5, for example.
Unused time from Team Preview should NOT be included with the 5 minute Your Time as usable selection time. For example, if I take 30 seconds at Team Preview, I should still only have 5 minutes of Your Time starting at turn 1, not 5 minutes + 60 unused seconds.
If Your Time < selection time (45 seconds), the player should still have the full selection time (45 seconds) to input their move. If Your Time reaches 0 in-game, that final turn can be completed; the game ends AFTER that current turn's end-of-turn effects, but BEFORE the start of the next turn. That is, if Your Time is not 0 before the start of the turn, the battle should continue. See the linked timestamp here for an example.
The +10 seconds of Your Time for animations is not something I agree with. In long, drawn-out games (situations where Your Time would be impactful), if a player chooses their move in under 10 seconds, they end up gaining Your Time, which is literally the opposite of what we want to happen. I am fine with using +10 seconds of selection time to account for animations, but adding it to the total Your Time just doesn't make sense to me. Pokemon Showdown already expedites the process of move selection significantly compared to cart. For example, a player can switch with a single click on Pokemon Showdown, while that same action takes several inputs in-game on cart. Because you're inherently saving time, I think 10 seconds is far too much extra, and defeats the purpose of the Your Time implementation in the first place. Here is an example of what I mean.
There are several issues with the current implementation of the timer used in "Your Time"-based VGC timers. As a summary of how it should work:
Current Issues: