That's an important consideration, and one I'm a bit embarrassed to admit I haven't put as much thought into as I should.
But lets give this a try:
I suppose one benefit would be more realism, but that has nothing to do with possible impact upon gameplay.
In the wild, horizontal gene transfer between microbes allows for the acquisition of beneficial traits, such as resistance to toxins. It can also be used as a mechanism to transfer "parasites".
Perhaps it could be incorporated into the upgrade system somehow? I see upgrades mentioned a lot. Maybe trading DNA helps accelerate the process? Maybe it's a fast way to gain new (random) agent types? Are there any evolutionary advantages the trading of which wouldn't completely mess up the game?
There's also the possible strategy of luring cells in to receive gene transfer and then prey on them instead. This could also be used against the player, though it'd have to have a lot of potential benefit to be worth the risk.
Interesting suggestions. I think if it were to give you more mutation points then there would have to be a risk to using it.
As a purely off the top of my head idea I guess maybe it could be more mutation points vs risk of infection. So maybe normally you get 5 mutation points in the editor (numbers for illustration only) and then each time you gene transfer you get 1 more (up to a max of 8) but there is also the chance you will catch a virus when you do it which will damage your cell. That would be an interesting mechanic.
Maybe you get to enter the editor after you get a certain amount if dna points, and you get them by reproducing (bonus points if done sexually), transfering dna, and maybe engulfing a nucleus/bacteria.