Why not just say that you're not allowed to form ties in F2 ? This would be very easy to spot if a bot is breaking the rule, and it would still be possible to implement tie defences so your bot can compete in F1 aswell...
Also I think a grey area rule that sais you can only use "exploits" in F1... so once a dirty trick is deemed too powerfull it's restricted to F1...
And I still think -8 shots need a charge time before being able to fire, or should only contain the part of your DNA you've charged when you fire the shot, or something like that.
Viruses and -8 shots are very similar, and both have the purpose of getting your DNA into someone else. But a virus will take ages to charge just a single gene, and it will be fired in a random direction, it's expensive to fire the virus, and slime will stop it. A -8 shot can be fired instantly containing 32000 pb with no charge time, no added costs, you can aim the shot, it can contain more than one gene, and the only disadvantage is that you need to be closer to the oponent and follow up with mem shots to force reproduction. And mem shots can be blocked by poison, but I think it was something like 200 poison to stop 1 mem shot...
The uses for viruses just seems very narrow compared to raping... I have a hard time imagining anything I could use a virus for in a league fight... I'm sure there's some way it could still be usefull, maybe as a suplement to raping... but still, I much prefered viruses since you had to think about how you where building them, making them as short as possible, nothing was added unless it was nessesary. Now it just seems too easy...
Not saying I have a great idea for fixing this, but IMO something need to be done