I haven't had any "middle management" settlers since moving from Civ I. Those were always very annoying, and one of the reasons I started clicking on my settlers at the end of every turn. Maybe MGE has accedentally reincluded that problem
As for the loss of of an extra engineer/settler turn, there is a way around that (Xin Yu had a post a long time ago about how to engineer transform in 1 turn using 20 engineers, not quite sure where that is off hand atm). Alternatives of that would be to try and have certain preworked units paired with unworked units so that the total amount of work of the 2 units adds up to the total work needed. For example, I like to have 2 engineers and a settler irrigate 2 squares every 2 turns (2x2 + 2x2 + 2x1 = 10). The settler bounces between the 2 engineers so that each turn it(1 unit of work) adds the 5th turn of work to the 2nd turn engineer (4 units of work).
Also, when more than 1 unit is working on a tile, you can lose an extra turn if the wrong unit goes first. An example would be an engineer(1 turn = 2 units) and a settler (1 turn) irrigating. If the settler goes first, total work is 1x2 (eng) + 2x1 (settler) = 4, and the engineer is needed to reach 5 (2x2 + 2x1 = 6). If the engineer goes first, however, the engineer finishes the work (2x2 + 1x1 = 5) and the settler is free to move this turn, although it loses its 1 turn of work.
I've never really tried to figure out how to use 3 units on the same time doing the same thing, since I almost always have many things I need done and I do have a way to minimize lost work.
Of course if you have several things you need to do to a tile, you can combine them effectively. One of my favorites in OCC is to start 2 engineers teraforming a grassland to a hill, while taking a settler and set him to mining on the same tile, so that the first 2 engineers create hills, the settler mines the hills (instead of creating a forest). Also if necessary, I'll have 2 engineers railroading the tile while it is still a grassland. All in all, I have 5 units working a grassland tile - 2 railroading, 2 transforing to hills, and 1 mining, and a grassland with road becomes a railroaded, mined hill in a timely manner
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Sleep is a luxury and I don't have Shakespeare's Theatre in my back yard.