No right or wrong answer, all depends on where you are in the game. Like Thief said, I focus on upgrading whatever the LE is at the moment, but after the free unit period ends, I go back and upgrade my boost buildings while I save up, then upgrade the costliest LE building I have (AMR) or can afford. So in the case of the TM, I doubt I will go back to upgrade it after the free unit period unless I get done with my other LEs that are a better return for me. My nanos and space centers are never higher than lv 1 because I use them as cash. Too long to upgrade vs the LEs. I think I stopped upgrading my non LE cash buildings after the jinai facility came out.
Need to keep in mind amount of time each building will take to upgrade. Not saying it is the only factor but definately needs consideration. I try to get every building to level 4 just because upgrades are so quick till then.
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