Legion's loyalty mission, the biggest glimpse into the geth we get in ME2, is built on the geth having a difference of opinion.
How does one have an opinion if they aren't an individual in some capacity?
The problem is that the writers didn't really think through what it means to be a gestalt. Their idea was simple: geth AI is basically distributed intelligence, so the more geth network the more processing power they have, and the more they come to resemble what we recognize as intelligence. The idea they were going for with the heretics was that essential the Geth do not have one single gestalt, nor do they want one - rather they have vast networks on physically separate "platforms" that interact with one another. Put another way, the geth had "individuals" but not exactly at the program level. There was a kind of conceptual lowest common denominator below which the network wouldn't be able to make decisions, but gestalts basically formed organically and were separate but apart.
The problem is that they don't think this through. Legion is not a unatiry being - it's a collection of multiple programs despite a unatiry form, and it's not clear how this works. L'Etoile seems to treat these constituent units as somehow having self-awareness - as being actual decision making units rather than just governed by some stochastic process, but that's nonsensical. There really isn't a paradigm by which to understand what they wanted to execute.
I found the Dyson sphere concept to be poorly explained, insofar as it did not make it clear what would happen to this arrangement.
All of this conceptually, of course. ME2 mixed it up with argle-bargle science.