Manual abilities work better if the units last a fair bit longer in combat than they do now. In other games with units that have multiple abilities, it is generally done on a smaller scale, with fewer amounts of units and in combat they can last up to 10 seconds. In this amount of time it is usually easier to select the individual units (or groups) and fire the relevant abilities. with larger amounts of units it gets a lot clustered and very time consuming to try and quick fire certain abilities when most individual units last only a few seconds at best.
Dawn of War / Company of Heroes has certain units in squads of multiple individuals. Each individual can be killed independently but allows for an easier time using abilities (using this system the game allows for a relatively large amount of individuals to make up for scale but ease in being able select the relevant units.
Auto-casting could be another way to help with some things, especially with some of the support units such as shamans as having to move through several groups of units to cast each ability one group at a time is tedious and often takes far longer to do on average than how long either some battles last or how long the specific units last.
A lot of the more complicated work can be made easier to carry out with an improved UI and command and control system; features such as auto-casting would make support roles easier, hot keys to quickfire all of the selected units 1st offensive ability at a target (or to seek nearest target if the order is issued on the ground etc.) could alleviate combat casting.
In my own opinion I tend to prefer to spend most of my time employing strategy; setting up build orders, destinations and general troop movement, but in quick combat like this it does become challenging to have to activate individual groups of units' abilities in order to increase combat efficiency because as combat can draw itself out if there are large streams heading towards each other in a lot of cases and use of abilities can be a large factor, doing so limits my abilities to go back onto each factory and set more things to get built to replace a completed build order and to replace fallen units. Doing the latter requires valuable combat time in the first place and so makes the game a lot harder than it needs to be, especially against an AI who can do both simultaneously.
In short I am thoroughly enjoying this game, an interesting RTS experience to say the least and I do hope the game to get polished up before release
