Ability damage does make for neat poisons, but it doesn't make for very threatening diseases IMO -- every day you take ability damage that you recover from on a daily basis anyway, oh no. The rules for disease could use an overhaul. Unfortunately, I'm really not sure how best to do it aside from narratively off the top of my head.
Poison, OTOH, has a decent basis, and ability damage and drain make great threats, and the existing status-based poisons are a good start on that option -- but poisons based on HP damage, both lethal and subdual, have their place too. I'll agree with the sentiment that having only two-stage, one-minute-interval poisons is too limiting and unrealistic, though probably for simplicity's sake any given poison should have the same interval between stages (so you can describe a poison as being a three-stage hour-interval poison or a five-stage round-interval poison). The game could also differentiate between poisons where what happens at each stage is fixed and poisons whose effects must be suffered in order; for example, a three-stage minute-interval poison could either always attempt to deal 1d4 Str damage at stage 1, 2d4 Str damage at stage 2, and 2d4 Str drain at stage 3... or it could be defined as 1d4 Str on the first failed save, 2d4 Str damage on the second failed save, and 2d4 Str drain on a third failed save.
Let us never speak of ravages and afflictions again. -- Pteryx