I don't care if "99%" is included, I just don't think it was a failure that is was NOT included. To discuss the Geth/Quarian presentation on the level you are is similar to discussing the romances by the time spent on the love scenes - its an incredibly petty way to look at the presentation. The player has to understand these two factions and eventually decide on one or to resolve the conflict. One of them, the Geth, has already joined or become enslaved by the Reapers, an enemy that the player actively fights against. And the player has to trust that this faction won't become enslaved by the Reapers later on, as the Rachni may have earlier.
Players already understand that the Geth almost wiped out the Quarians, 99% dead or war over within a year will not change their perception.
BUT, if you're going to advocate for clarity, ie. 99% and "slaughter" on the Quarian side, to be intellectually honest you should be arguing for percentages and descriptions on the Geth side. Otherwise, you're advocating for a bias.
Way ahead of you.
ME2 codex, Geth culture:
The most remarkable aspect of geth culture is that it may not exist at all. Geth are a network intelligence; a single entity in myriad bodies. They share data with one another, whether discrete facts or "memories": audiovisual recordings of experiences and logs of thought-processes. Any event experienced by one geth is uploaded to the group mind, so that all geth, everywhere, "remember" such an event as if they'd experienced it themselves.
No one knows whether the geth develop personalities as organic-created AIs do. If an organic-designed AI is transferred into another quantum bluebox, its personality is reset. Most geth programs transfer from one hardware platform to another constantly; if a geth needs to travel to another star, it downloads into a starship body. If it needs to replace a piece of malfunctioning hardware, it downloads into a small body with hands. If geth are reset at transfer, it would make development of individual personalities unlikely.
Records of the quarian war suggest the geth have no concept of self-preservation. They do not flinch from gunfire, and do not hesitate to sacrifice themselves if it allows their fellows an advantage. Thousands of mobile platforms were expended assaulting quarian positions, but file-sharing between platforms ensured their memories and experience would not be lost. Geth are therefore immortal; if their hardware is destroyed, archival copies of their programs and databases can be downloaded into a new body.
With the gap in contact between the quarian war and the arrival of Sovereign, the only proven fact about the geth is that they were isolationists for centuries. They never ventured outside the Perseus Veil, but no organic ship that entered their territory ever returned.
They didn't see fit to package this codex entry in ME3 for whatever reason...
While we're at it, maybe we could add dialogue addressing the impact of their centuries of isolationism on prospective peace talks and two years of inaction against the heretics instead of tucking the only mention of the former away on the map description of Haestrom and barely acknowledging the existence of the latter at all.
I know you're trying to draw an equivalency, but the loss of Geth runtimes or hardware really cannot be directly compared to the death of individually-sapient organics. One experiences total, permanent loss of functionality with all information stored in memory irrevocably destroyed; the other experiences reduced functionality until additional hardware is added to the network and possible memory loss based on what's archived where. It's only with the complete destruction of their network that the latter truly dies. Did that ever happen during the Morning War?