Since enhancement bonuses of projectile weapons and ammunition do not stack, making your arrows +1 is no benefit once you have a magic bow. This is a problem with magic ammunition in general: finding it is no longer exciting once you have a magic bow. It's an unfortunate problem, and I can't think of a way to fix it.
Anyway, Enhance Arrows addresses the problem by juicing your arrows with other benefits like flame, frost, and shock. Pretty fun stuff. At 9th level, you add anarchic, axiomatic, holy, or unholy to your arrows, as long as you don't choose one that is opposed to your alignment. Since you choose once per day, the ability favors neutrality, because a Neutral character can choose any of the four.
Is it really the intention to give more utility to neutral characters? Shouldn't there be something to compensate non-neutral characters in that case? I was wondering if this could work like a cleric's channel energy, so that if an arcane archer is neutral on a given axis, she has to choose once forever which side of the axis will benefit her arrows. That way all archers have a choice between exactly two of the four alignment-based properties. For example, a Lawful Good archer can choose each day to make her arrows holy or axiomatic. Maybe this seems nit-picky, but the designers clearly felt this utility was significant, or they wouldn't have limited the choice to once per day.
Which makes me wonder, would the added utility really be all that unbalancing if you could choose the properties every round? The ability seems designed to frustrate the way it is. If you're Lawful Good, you can't fire a holy arrow at a devil just because you already chose axiomatic earlier in the day?
I assume that the alignment properties stack with the flame, frost, and shock properties, since it doesn't state otherwise.
Yes, I think that neutral characters have too many advantages. Your option to make it work like cleric is a good one I think.