Increase the cooldown and make it an ultimate ability. Or in other words, you empower 1 of your 3 or 4 skills and it has an ultimate effect, giving you 3 or 4 different ultimates (shared cooldown).
Another application would be very similar the the Invoker in DOTA, in that you combine skills to produce results. I think they went over the top with the possibilities for invoker, but for demigod, keep it simple (2 combos). In essence, click combo (ult) button, select skill 1 and skill 2 results in ultimate 1. After cooldown, click combo (ult) button, select skill 2 and skill 3 results in ultimate 2 and so on.
Now that I'm brainstorming, imagine a tree below on your GUI.
---------
|........|
|skill 1|
|........|...-----------
---------..|.............|
.............|Combo 1|
---------..|.............|....----------
|........|...---------.....|.............|
|skill 2|...................|Ultimate|
|........|...-----------...|............|
---------..|.............|...---.-------
.............|Combo 2|
---------..|.............|
|........|...-----------
|skill 3|
|........|
---------
[couldn't get my graphic to upload

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In this example, combo 1 would be a advanced spell based on skill 1 and 2. The availability of combo 1, the strength of the combo, cooldown, and cost may be dependent on the ranks put into skill 1 and 2. Likewise combo 2 will be based on skills 2 and 3.
The ultimate would require ranks in all three skills, and would be some major kick ass skill with cool animation. Again, strength, cooldown and cost would depend on the # of ranks in skills 1-3.
I know this differs from the current system and I'm only thinking outload so please don't rip it to shreds.