I agree that aging must be very careful. However, I'd contest that with Pokemon, at least, a balance needs to be found. It's kind of difficult to write credible stories about ten-year-olds falling in love in my opinion, but on the other hand aging and changing them too much can lose you a lot of audience as well.
As for why I'd write a shipping story where the relationship is not central: I like epic tales. XD And I'd say that, when done well, the two stories can mingle with exceptional results. That's what I've seen. Think of it as a dual-typed Pokemon. It gives some strengths to your overall story and some weaknesses - what determines if this is good or not is net gain or loss of weaknesses and strengths. Sableye/Spiritomb = the ultimate "Epic Legendary Battle Mixed with a Shipping Fanfiction" Pokemon.
As for why I'd write a shipping story where the relationship is not central: I like epic tales. XD And I'd say that, when done well, the two stories can mingle with exceptional results. That's what I've seen. Think of it as a dual-typed Pokemon. It gives some strengths to your overall story and some weaknesses - what determines if this is good or not is net gain or loss of weaknesses and strengths. Sableye/Spiritomb = the ultimate "Epic Legendary Battle Mixed with a Shipping Fanfiction" Pokemon.