This is a long topic. There are very few generalities here (which I know you understand, but it's worth reiterating regardless) because of how different all of the spirits are. But here are some thoughts regardless:
You will almost never reach the highest levels of your innate powers. Typically, doing so requires playing almost the maximum number of card plays. And that of course means that you need to have powers with the elements you need and the energy to play them all. The final levels of the innate powers are rarely worth that much aggravation. The sweet spot is usually the middle levels which are powerful enough to be interesting, but not so difficult to achieve.
Innate powers are not free. They don't cost any card plays, and they don't cost energy (with the exception of the final level of Serpent Rouses In Anger), but they cost you in flexibility. If you want to gain the effect then it restricts what powers you are taking and when you are playing certain cards. That can be a significant cost, but again you are getting an effect without sacrificing a card play or energy, which is extremely valuable.
Possibly most important of all:
Elements are not used just for activating the innate powers of the spirits. Activating the maximum effects of any major power (and some minor powers) requires meeting elemental thresholds. Many of these are significantly more powerful than any innate. (Cleansing Flood, for example, adds +10 damage if you have 4 water). Many of them are also easier to achieve, especially as they usually have the elements their threshold requires. If you pick up a Major power late game, you may not have time to aquire cards with the elements needed to trigger its threshold, but if you spent the game focusing on a select group of elements, then you will likely be able to find a power that you are already able to fully activate. This is, I think, where the real power of elements comes into play. Innates are nice, but mostly they should be treated as guides so that when the time comes you will be able to utilize your major powers to their maximum effect.