I use to go with the 3 free constructors before turning to the malevolent tree. Depending on how many asteroid mines you get from them, the benefit is larger (and earlier), than the +10 of the malevolent trait. But you are correct, +10 all production and especially the following +100% ship manufacturing is big.
They changed the ideology point values. Death furnace and temple of enlightenment only give you .3 per turn as opposed to the advertised 1 per turn. The temple itself is only as good as a citizen besides the +3 adjacency. For a player unique they are not that big a deal anymore.
I allways liked the benevolent colonizers. Though this depends on how crowded your galaxy is.
the +5 science on all planets was ok-ish before crusade, not it is amazing.
What I am growing to appreciate is the pragmatic starbase tree. With starbase range and mining bonusses it is quite ok. The increased shipyard distance can be helpful early on.