While I feel EE2 was far too easy for any server I play on - people are allowed their opinions.
I'm not sure how anyone would attempt to defend the collector-condenser flowers though.
Self-contradiction, much?
Although, it wasn't the flowers that were the real problem, IMO. It was that you could easily do loops (blaze rods, dark rooms, etc.)
The bits bout EE2 that were acceptable were the exchange, although I would like to see limitations on later versions. I dislike that someone can turn almost anything into almost anything else instantly once you had a bit of power stored up in your star, and I would like either that you can only change items based on say... properties (a bit like thaumcraft), tier (to stop getting difficult things just by clicking on easy things), or have set transmutes which I wouldn't mind being powerful as long as the powerful ones were limited in some way (variety, path to unlock, number of uses, anything really)
Unfortunately, the charm of EE2 was exactly that - that you could trade anything for anything else.
Properties would either conflict with Thaumcraft, or be a duplicate of it.
Tiers would only work as long as NOTHING can convert between tiers. (coal -> diamonds, for example) This includes other mods, and as such is impossible.
Set transmutes... Would generally be exploitative or useless, I think. Could you give an example that would be useful that couldn't be exploited?
I don't know what you mean by "variety".
As for a path to unlock - remember that EE2 had a rather large setup cost, and that most people playing with Thaumcraft have everything useful unlocked.
Number of uses? Any transmute component that can be automated can be repaired or replaced automatically.
Not allowing automation? a) good luck. b) people probably simply wouldn't use it. It's the reason why almost no-one uses IC2 crops.