It sounds like the nature of the system is to allow players some granularity in their specialization as they level. The types of skills invested in at the Lieutenant rank will determine what kinds of more specialized skills are available at the Lieutenant Commander rank. Then, once a player invests enough skill points to become a Commander, they'll dig even further into their chosen specialty.
There's a lot more detail in the Ask Cryptic write-up, and you can even post questions directly to the devs in the forum thread linked to the article.
