In figuring out how many teams might be available for a hypothetical Intertoto, I noticed an interesting phenomena in countries with a large number of bots (which is almost every country). Because the draw is random, there will be some human v. human matchups in each round, a large number of human v bot matchups, and a large number of bot v bot matchups. This guarantees that one team in the human v human matchups will lose and be eliminated. While a bot team might upset an active team this is unusual.
As a result, you have round after round of roughly the same number of active teams being eliminated, while most have practically a bye. It would be like if a few were chosen to be thrown in the gladiator pit, while the main risk to most others is to be nicked while shaving.
The bots should not really be regarded as an integral part of the competition, but merely a way to fill out the field to a power of two. So my suggestion is to maintain the current random draw - but to make it bot-aware. This is quite simple.
If there are more bots than human teams remaining, then place balls for all the bot teams in one pot, and balls for all the human teams in another pot. Draw one team from each pot, until the human pot is emptied. Then draw pairs of bots from the bot pot to complete the field.
If there are more human teams than bots, then one team is drawn from each pot until bot pot is emptied, and the remaining humans are drawn against each other.
A few human teams will lose to their bot opponent, but otherwise they will be eliminated in a relatively few rounds.
Whether a team is a bot or not could be determined at the time of each draw. So if a bot gets an owner, or a team becomes a bot, it is treated based on its new status. There are relatively few teams that switch in a given week, and most will have been eliminated earlier, either because they were a bot, or a team on the road to becoming a bot.
A second change to the cup draw would be to balance the home and away games. After two teams are drawn, the team which has had fewer home games against human opponents will be selected as the home team. If the teams have had the same number of home games, then the site is drawn like usual.
Consideration could be given to using neutral sites for the final rounds (Sweet 16?)