Essentially, I think that when you drag out a selection bracket over a number of units, containing combat units, construction units and factories, it should only select the combat units.
If no combat units are present, the selection marquee works normally. You can select groups of construction units, groups of factories, etc.
Now, to allow people to still do it the old way should they wish (sometimes you might want too), I suggest that holding a button while drag-selecting should allow normal behaviour (that is, selects everything within the marquee).
I say that the new version should be the default, and the button should be the alternate simply because after playing SupCom competitively for a while, which has this function, it really is just a far superior selection method.
Generally when you are ordering large amounts of units, you only want to select your combat troops. Quite often you will accidentally select a con unit and move him away from his task, losing his construction que and possibly whatever he was building. This also happens with factories, when I find myself regularly having to reset rally points because I've given the factory an accidental new rally point while moving groups of units.
This function allows you to safely just drag a marquee over your whole base and select any combat units there without worrying about disrupting your economy. It also makes it easier to run both combat manuevres and reclaiming/repairing operations at the frontlines.
On the other hand, when you are selecting construction units and factories, you are far more commonly doing this in a one-by-one basis due to the nature of the units, and the selection system (I most commonly select con units and factories using ctrl+b anyway).
Again, sorry if you can already do this and I'm just not aware of it. I'm starting to play spring competitively a lot more now that we're beta testing IW, and I'm missing a lot of abilities that were second nature in SupCom.
EDIT: Actually, if someone was going to work on this, I think a more robust system would be to allow mod-makers to be able to set what units are selected in a marquee when a certain button is pressed. For example, S44 could make it that when you press 'A' and drag a selection box, only aircraft (or, only fighters) are selected. IW could make it only infantry are selected when you depress 'I', etc. And obviously you'd be able to do all of the above suggested stuff too. (note: still think 'only select combat units if they are present should be default though
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