Currently the only choice in the Citadel Upgrade trees is "which upgrade to I take NOW" because eventually you will get them all.
I would feel a greater sense of personalization if in every tier of upgrades there were a couple of options that gave a this OR that option.
These could be a part of the regular upgrade trees, or separate options that are given as you increase in tier regardless of previous uprades chosen.
One of the following buildings becomes an essential blueprint X or Y.
Blight is faster and more dangerous, but blight bonuses are also better OR You gain a bonus (like some crystal sparkdew) for defeated blight cysts)
Caches and Events require more resources but have better rewards OR take less resources but require more time.
More chance for bonus yield from mutated trees OR bonus yield from giant resource nodes.
The list goes on an on, but the important thing is they should be things that dont feel mandatory, and that the choice to go with them affects your view of what your company is about.
I think this would be a nice addition as long as there's a respec option. Gives an option to point your playstyle towards a specific playstyle for multiple towns. Might be a bit redundant though.
Isn't this like what embark bonus are? Are you able to change your decision? What if you make the "wrong" decision, and can't change it?