I've said this before, the only limited resource in SupCom is the player's attention. (Well, that and unit cap.)
When designing a game like SupCom, you have to be conscious of what things take up player attention, how much, and what benefits it brings.
So on the one hand, incentivising manual reclaim is a good thing, for competitive/strategy reasons - you make the player spend attention in order to gain an advantage.
However, when you think about designing a cool and fun game, manual reclaim is a very poor idea, especially since most manually reclaimed items do not appear until you zoom in to a certain level.
So yes, you want the game to require players to spend attention to gain an advantage. This means players who know how and where to focus their attention, and who can spend their attention on many things at once, will be more effective. (this is a more general understanding of the "higher apm = more skill" thing.)
However! To make a fun and cool game, that's fun to play and spectate, you want to make all the attention-focusing things cool and fun, and you want all the boring things to be automatically managed. So the sorts of things you should force players to micro to gain an advantage should generally be combat focused:
- Overcharge
- Unit micro, unit tactics.
- TMLs, Nukes
- Activated powers
- Retreating damaged units for repair
etc.
When we think of a game of SupCom, we want the screen to be zoomed into awesome combat as much as possible. We don't want the combat to be completely manageable at strategic zoom, and then have players zoomed in only for clicking rocks, or placing their structures in the perfect layout etc.
So yeah, if you want to have micro in the game, to give an avenue to mechanical skill, then add activated powers, units that perform better when microed, tactical advantages due to unit formation / positioning, etc. Don't spend players' precious attention on boring mechanics like structure adjacency and manual reclaim.